Publications by authors named "Phillip L Geissler"

87 Publications

Assessing long-range contributions to the charge asymmetry of ion adsorption at the air-water interface.

Chem Sci 2020 Oct 5;11(43):11791-11800. Epub 2020 Oct 5.

Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.

Anions generally associate more favorably with the air-water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this bias. Here we assess quantitatively the role that intrinsic charge asymmetry of water's surface plays in ion adsorption, using computer simulations to compare model solutes of various size and charge. In doing so, we also evaluate the degree to which linear response theory for solvent polarization is a reasonable approach for comparing the thermodynamics of bulk and interfacial ion solvation. Consistent with previous works on bulk ion solvation, we find that the average electrostatic potential at the center of a neutral, sub-nanometer solute at the air-water interface depends sensitively on its radius, and that this potential changes quite nonlinearly as the solute's charge is introduced. The nonlinear response closely resembles that of the bulk. As a result, the net nonlinearity of ion adsorption is weaker than in bulk, but still substantial, comparable to the apparent magnitude of macroscopically nonlocal contributions from the undisturbed interface. For the simple-point-charge model of water we study, these results argue distinctly against rationalizing ion adsorption in terms of surface potentials inherent to molecular structure of the liquid's boundary.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d0sc01947jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8162909PMC
October 2020

Phase Diagram of Active Brownian Spheres: Crystallization and the Metastability of Motility-Induced Phase Separation.

Phys Rev Lett 2021 May;126(18):188002

Department of Chemistry, University of California, Berkeley, California 94720, USA.

Motility-induced phase separation (MIPS), the phenomenon in which purely repulsive active particles undergo a liquid-gas phase separation, is among the simplest and most widely studied examples of a nonequilibrium phase transition. Here, we show that states of MIPS coexistence are in fact only metastable for three-dimensional active Brownian particles over a very broad range of conditions, decaying at long times through an ordering transition we call active crystallization. At an activity just above the MIPS critical point, the liquid-gas binodal is superseded by the crystal-fluid coexistence curve, with solid, liquid, and gas all coexisting at the triple point where the two curves intersect. Nucleating an active crystal from a disordered fluid, however, requires a rare fluctuation that exhibits the nearly close-packed density of the solid phase. The corresponding barrier to crystallization is surmountable on a feasible timescale only at high activity, and only at fluid densities near maximal packing. The glassiness expected for such dense liquids at equilibrium is strongly mitigated by active forces, so that the lifetime of liquid-gas coexistence declines steadily with increasing activity, manifesting in simulations as a facile spontaneous crystallization at extremely high activity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.126.188002DOI Listing
May 2021

Weak scaling of the contact distance between two fluctuating interfaces with system size.

Phys Rev E 2020 Dec;102(6-1):062801

Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.

A pair of flat parallel surfaces, each freely diffusing along the direction of their separation, will eventually come into contact. If the shapes of these surfaces also fluctuate, then contact will occur when their centers-of-mass remain separated by a nonzero distance ℓ. An example of such a situation is the motion of interfaces between two phases at conditions of thermodynamic coexistence, and in particular the annihilation of domain wall pairs under periodic boundary conditions. Here we present a general approach to calculate the probability distribution of the contact distance ℓ and determine how its most likely value ℓ^{*} depends on the surfaces' lateral size L. Using the Edward-Wilkinson equation as a model for interfaces, we demonstrate that ℓ^{*} scales weakly with system size, i.e., the dependence of ℓ^{*} on L for both (1+1)- and (2+1)-dimensional interfaces is such that lim_{L→∞}(ℓ^{*}/L)=0. In particular, for (2+1)-dimensional interfaces ℓ^{*} is an algebraic function of logL, a result that is confirmed by computer simulations of slab-shaped domains formed under periodic boundary conditions. This weak scaling implies that such domains remain topologically intact until ℓ becomes very small compared to the lateral size of the interface, contradicting expectations from equilibrium thermodynamics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.102.062801DOI Listing
December 2020

Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes.

J Phys Chem B 2020 07 7;124(28):5884-5898. Epub 2020 Jul 7.

Department of Chemistry, University of California, Berkeley, California 94720, United States.

The maintenance of heterogeneous lipid compositions among cellular membranes is key to biological function. Yet, even the simplest process that could be responsible for maintaining proper lipid distributions, passive lipid exchange of individual molecules between membranes, has eluded a detailed understanding, due in part to inconsistencies between experimental findings and molecular simulations. We resolve these discrepancies by discovering the reaction coordinate for passive lipid exchange, which enables a complete biophysical characterization of the rate-limiting step for lipid exchange. Our approach to identify the reaction coordinate capitalizes on our ability to harvest over 1000 unbiased trajectories of lipid insertion, an elementary step of passive lipid transport, using all-atom and coarse-grained molecular dynamics simulations. We find that the reaction coordinate measures the formation and breakage of hydrophobic contacts between the membrane and exchanging lipid. Consistent with experiments, free energy profiles as a function of our reaction coordinate exhibit a substantial barrier for insertion. In contrast, lipid insertion was predicted to be a barrier-less process by previous computational studies, which incorrectly presumed the reaction coordinate to be the displacement of the exchanging lipid from the membrane. Utilizing our newfound knowledge of the reaction coordinate, we formulate an expression for the lipid exchange rate to enable a quantitative comparison with experiments. Overall, our results indicate that the breakage of hydrophobic contacts is rate limiting for passive lipid exchange and provide a foundation to understand the catalytic function of lipid transfer proteins.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.0c04139DOI Listing
July 2020

Lattice Models for Protein Organization throughout Thylakoid Membrane Stacks.

Biophys J 2020 06 1;118(11):2680-2693. Epub 2020 May 1.

Department of Chemistry, University of California, Berkeley, California; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California. Electronic address:

Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by microscopy and fluorescence spectroscopy and demonstrated by computer simulations of a coarse-grained model. The architecture of thylakoid membranes, however, also provides opportunities for interlayer interactions that instead disfavor the high protein densities of ordered arrangements. Here, we explore the interplay between these opposing driving forces and, in particular, the phase transitions that emerge in the periodic geometry of stacked thylakoid membrane disks. We propose a lattice model that roughly accounts for proteins' attraction within a layer and across the stromal gap, steric repulsion across the lumenal gap, and regulation of protein density by exchange with the stroma lamellae. Mean-field analysis and computer simulation reveal rich phase behavior for this simple model, featuring a broken-symmetry striped phase that is disrupted at both high and low extremes of chemical potential. The resulting sensitivity of microscopic protein arrangement to the thylakoid's mesoscale vertical structure raises intriguing possibilities for regulation of photosynthetic function.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2020.03.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264851PMC
June 2020

Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids.

Phys Rev Lett 2019 Sep;123(13):135701

Department of Chemistry, University of California, Berkeley, California 94720, USA and Erwin Schrödinger Institute for Mathematics and Physics, University of Vienna, Boltzmanngasse 9, Wien 1090, Austria.

Lattice mismatch can substantially impact the spatial organization of heterogeneous materials. We examine a simple model for lattice-mismatched solids over a broad range of temperature and composition, revealing both uniform and spatially modulated phases. Scenarios for coexistence among them are unconventional due to the extensive mechanical cost of segregation. Together with an adapted Maxwell construction for elastic phase separation, mean field theory predicts a phase diagram that captures key low-temperature features of Monte Carlo simulations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.123.135701DOI Listing
September 2019

Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations.

J Chem Phys 2018 Jun;148(22):222823

Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (1999)]: Long-wavelength solvent response underlying finite size effects should be well described by reduced models like dielectric continuum theory, whose size dependence can be calculated straightforwardly. Applied to an ion in a periodic slab of liquid coexisting with vapor, this approach yields a finite size correction for solvation free energies that differs in important ways from results previously derived for bulk solution. For a model polar solvent, we show that this new correction quantitatively accounts for the variation of solvation free energy with volume and aspect ratio of the simulation cell. Correcting periodic slab results for an aqueous system requires an additional accounting for the solvent's intrinsic charge asymmetry, which shifts electric potentials in a size-dependent manner. The accuracy of these finite size corrections establishes a simple method for a posteriori extrapolation to the thermodynamic limit and also underscores the realism of dielectric continuum theory down to the nanometer scale.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.5020563DOI Listing
June 2018

Robust nonequilibrium pathways to microcompartment assembly.

Proc Natl Acad Sci U S A 2018 06 4;115(25):6341-6346. Epub 2018 Jun 4.

Department of Chemistry, University of California, Berkeley, CA 94720

Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that posit microcompartments as stable equilibrium arrangements of the constituent proteins. Here we describe a different mechanism for microcompartment assembly, one that is fundamentally nonequilibrium and yet highly reliable. This pathway is revealed by simulations of a molecular model resolving the size and shape of a cargo droplet and the extent and topography of an elastic shell. The resulting metastable microcompartment structures closely resemble those of carboxysomes, with a narrow size distribution and faceted shells. The essence of their assembly dynamics can be understood from a simpler mathematical model that combines elements of classical nucleation theory with continuum elasticity. These results highlight important control variables for achieving nanoscale encapsulation in general and for modulating the size and shape of carboxysomes in particular.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1802499115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016822PMC
June 2018

Rare behavior of growth processes via umbrella sampling of trajectories.

Phys Rev E 2018 Mar;97(3-1):032123

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space, in terms of their typical and atypical trajectories. Thus key features of growth processes can be insensitive to the precise form of the rate constants used to generate them, recalling the insensitivity to microscopic details of certain equilibrium behavior. We obtained these results using a sampling method, inspired by the "s-ensemble" large-deviation formalism, that amounts to umbrella sampling in trajectory space. The method is a simple variant of existing approaches, and applies to ensembles of trajectories controlled by the total number of events. It can be used to determine large-deviation rate functions for trajectory observables in or out of equilibrium.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.97.032123DOI Listing
March 2018

Exploiting Chromophore-Protein Interactions through Linker Engineering To Tune Photoinduced Dynamics in a Biomimetic Light-Harvesting Platform.

J Am Chem Soc 2018 05 9;140(20):6278-6287. Epub 2018 May 9.

Kavli Energy NanoSciences Institute , Berkeley , California 94720 , United States.

Creating artificial systems that mimic and surpass those found in nature is one of the great challenges of modern science. In the context of photosynthetic light harvesting, the difficulty lies in attaining utmost control over the energetics, positions and relative orientations of chromophores in densely packed arrays to transfer electronic excitation energy to desired locations with high efficiency. Toward achieving this goal, we use a highly versatile biomimetic protein scaffold from the tobacco mosaic virus coat protein on which chromophores can be attached at precise locations via linkers of differing lengths and rigidities. We show that minor linker modifications, including switching chiral configurations and alkyl chain shortening, lead to significant lengthening of the ultrafast excited state dynamics of the system as the linkers are shortened and rigidified. Molecular dynamics simulations provide molecular-level detail over how the chromophore attachment orientations, positions, and distances from the protein surface lead to the observed trends in system dynamics. In particular, we find that short and rigid linkers are able to sandwich water molecules between chromophore and protein, leading to chromophore-water-protein supracomplexes with intricately coupled dynamics that are highly dependent on their local protein environment. In addition, cyclohexyl-based linkers are identified as ideal candidates to retain rotational correlations over several nanoseconds and thus lock relative chromophore orientations throughout the lifetime of an exciton. Combining linker engineering with judicious placement of chromophores on the hydrated protein scaffold to exploit different chromophore-bath couplings provides a clear and effective path to producing highly controllable artificial light-harvesting systems that can increasingly mimic their natural counterparts, thus aiding to elucidate natural photosynthetic mechanisms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.7b13598DOI Listing
May 2018

Reconfigurable Printed Liquids.

Adv Mater 2018 Apr 24;30(16):e1707603. Epub 2018 Mar 24.

Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.

Liquids lack the spatial order required for advanced functionality. Interfacial assemblies of colloids, however, can be used to shape liquids into complex, 3D objects, simultaneously forming 2D layers with novel magnetic, plasmonic, or structural properties. Fully exploiting all-liquid systems that are structured by their interfaces would create a new class of biomimetic, reconfigurable, and responsive materials. Here, printed constructs of water in oil are presented. Both form and function are given to the system by the assembly and jamming of nanoparticle surfactants, formed from the interfacial interaction of nanoparticles and amphiphilic polymers that bear complementary functional groups. These yield dissipative constructs that exhibit a compartmentalized response to chemical cues. Potential applications include biphasic reaction vessels, liquid electronics, novel media for the encapsulation of cells and active matter, and dynamic constructs that both alter, and are altered by, their external environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/adma.201707603DOI Listing
April 2018

A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity.

ACS Chem Biol 2018 03 9;13(3):793-800. Epub 2018 Feb 9.

Department of Chemistry , Ludwig-Maximilian-University Munich and Munich Center for Integrated Protein Science (CIPSM) , Butenandtstrasse 5-13 , 83177 Munich , Germany.

Optogenetics and photopharmacology are powerful approaches to investigating biochemical systems. While the former is based on genetically encoded photoreceptors that utilize abundant chromophores, the latter relies on synthetic photoswitches that are either freely diffusible or covalently attached to specific bioconjugation sites, which are often native or engineered cysteines. The identification of suitable cysteine sites and appropriate linkers for attachment is generally a lengthy and cumbersome process. Herein, we describe an in silico screening approach that is designed to propose a small number of optimal combinations. By applying this computational approach to human carbonic anhydrase and a set of three photochromic tethered ligands, the number of potential site-ligand combinations was narrowed from over 750 down to 6, which we then evaluated experimentally. Two of these six combinations resulted in light-responsive human Carbonic Anhydrases (LihCAs), which were characterized with enzymatic activity assays, mass spectrometry, and X-ray crystallography. Our study also provides insights into the reactivity of cysteines toward maleimides and the hydrolytic stability of the adducts obtained.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschembio.7b00862DOI Listing
March 2018

Mechanism of ion adsorption to aqueous interfaces: Graphene/water vs. air/water.

Proc Natl Acad Sci U S A 2017 12 21;114(51):13369-13373. Epub 2017 Aug 21.

Department of Chemistry, University of California, Berkeley, CA 94720;

The adsorption of ions to aqueous interfaces is a phenomenon that profoundly influences vital processes in many areas of science, including biology, atmospheric chemistry, electrical energy storage, and water process engineering. Although classical electrostatics theory predicts that ions are repelled from water/hydrophobe (e.g., air/water) interfaces, both computer simulations and experiments have shown that chaotropic ions actually exhibit enhanced concentrations at the air/water interface. Although mechanistic pictures have been developed to explain this counterintuitive observation, their general applicability, particularly in the presence of material substrates, remains unclear. Here we investigate ion adsorption to the model interface formed by water and graphene. Deep UV second harmonic generation measurements of the SCN ion, a prototypical chaotrope, determined a free energy of adsorption within error of that for air/water. Unlike for the air/water interface, wherein repartitioning of the solvent energy drives ion adsorption, our computer simulations reveal that direct ion/graphene interactions dominate the favorable enthalpy change. Moreover, the graphene sheets dampen capillary waves such that rotational anisotropy of the solute, if present, is the dominant entropy contribution, in contrast to the air/water interface.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1702760114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754757PMC
December 2017

Virtual Issue in Memory of David Chandler.

J Phys Chem B 2017 06;121(21):5309-5311

University of California, Berkeley.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.7b04830DOI Listing
June 2017

From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

J Phys Chem B 2017 02 18;121(4):671-682. Epub 2017 Jan 18.

Physik Department, Technische Universität München , 85748 Garching, Germany.

Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.6b10189DOI Listing
February 2017

Size-dependent protein segregation at membrane interfaces.

Nat Phys 2016 Jul 7;12(7):704-711. Epub 2016 Mar 7.

Department of Bioengineering, University of California, Berkeley, CA; UC Berkeley / UC San Francisco Graduate Group in Bioengineering, Berkeley, CA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA.

Membrane interfaces formed at cell-cell junctions are associated with characteristic patterns of membrane protein organization, such as E-cadherin enrichment in epithelial junctional complexes and CD45 exclusion from the signaling foci of immunological synapses. To isolate the role of protein size in these processes, we reconstituted membrane interfaces in vitro using giant unilamellar vesicles decorated with synthetic binding and non-binding proteins. We show that size differences between binding and non-binding proteins can dramatically alter their organization at membrane interfaces in the absence of active contributions from the cytoskeleton, with as little as a ~5 nm increase in non-binding protein size driving its exclusion from the interface. Combining in vitro measurements with Monte Carlo simulations, we find that non-binding protein exclusion is also influenced by lateral crowding, binding protein affinity, and thermally-driven membrane height fluctuations that transiently limit access to the interface. This simple, sensitive, and highly effective means of passively segregating proteins has implications for signaling at cell-cell junctions and protein sorting at intracellular contact points between membrane-bound organelles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nphys3678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5152624PMC
July 2016

Single-particle mapping of nonequilibrium nanocrystal transformations.

Science 2016 11;354(6314):874-877

Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.

Chemists have developed mechanistic insight into numerous chemical reactions by thoroughly characterizing nonequilibrium species. Although methods to probe these processes are well established for molecules, analogous techniques for understanding intermediate structures in nanomaterials have been lacking. We monitor the shape evolution of individual anisotropic gold nanostructures as they are oxidatively etched in a graphene liquid cell with a controlled redox environment. Short-lived, nonequilibrium nanocrystals are observed, structurally analyzed, and rationalized through Monte Carlo simulations. Understanding these reaction trajectories provides important fundamental insight connecting high-energy nanocrystal morphologies to the development of kinetically stabilized surface features and demonstrates the importance of developing tools capable of probing short-lived nanoscale species at the single-particle level.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aah4434DOI Listing
November 2016

Microscopic origin and macroscopic implications of lane formation in mixtures of oppositely driven particles.

Phys Rev E 2016 Aug 19;94(2-1):022608. Epub 2016 Aug 19.

Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.

Colloidal particles of two types, driven in opposite directions, can segregate into lanes [Vissers et al., Soft Matter 7, 2352 (2011)1744-683X10.1039/c0sm01343a]. This phenomenon can be reproduced by two-dimensional Brownian dynamics simulations of model particles [Dzubiella et al., Phys. Rev. E 65, 021402 (2002)1063-651X10.1103/PhysRevE.65.021402]. Here we use computer simulation to assess the generality of lane formation with respect to variation of particle type and dynamical protocol. We find that laning results from rectification of diffusion on the scale of a particle diameter: oppositely driven particles must, in the time taken to encounter each other in the direction of the drive, diffuse in the perpendicular direction by about one particle diameter. This geometric constraint implies that the diffusion constant of a particle, in the presence of those of the opposite type, grows approximately linearly with the Péclet number, a prediction confirmed by our numerics over a range of model parameters. Such environment-dependent diffusion is statistically similar to an effective interparticle attraction; consistent with this observation, we find that oppositely driven nonattractive colloids display features characteristic of the simplest model system possessing both interparticle attractions and persistent motion, the driven Ising lattice gas [Katz, Leibowitz, and Spohn, J. Stat. Phys. 34, 497 (1984)JSTPBS0022-471510.1007/BF01018556]. These features include long-ranged correlations in the disordered regime, a critical regime characterized by a change in slope of the particle current with the Péclet number, and fluctuations that grow with system size. By analogy, we suggest that lane formation in the driven colloid system is a phase transition in the macroscopic limit, but that macroscopic phase separation would not occur in finite time upon starting from disordered initial conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.94.022608DOI Listing
August 2016

Near-optimal protocols in complex nonequilibrium transformations.

Proc Natl Acad Sci U S A 2016 09 29;113(37):10263-8. Epub 2016 Aug 29.

Department of Chemistry, University of California, Berkeley, CA 94720; Biophysics Graduate Group, University of California, Berkeley, CA 94720; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.

The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. We describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. We show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of the protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1606273113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027427PMC
September 2016

The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation.

PLoS Comput Biol 2016 07 6;12(7):e1004982. Epub 2016 Jul 6.

Department of Chemistry, University of California, Berkeley, California, United States of America.

Tubular protrusions are a common feature of living cells, arising from polymerization of stiff protein filaments against a comparably soft membrane. Although this process involves many accessory proteins in cells, in vitro experiments indicate that similar tube-like structures can emerge without them, through spontaneous bundling of filaments mediated by the membrane. Using theory and simulation of physical models, we have elaborated how nonequilibrium fluctuations in growth kinetics and membrane shape can yield such protrusions. Enabled by a new grand canonical Monte Carlo method for membrane simulation, our work reveals a cascade of dynamical transitions from individually polymerizing filaments to highly cooperatively growing bundles as a dynamical bottleneck to tube formation. Filament network organization as well as adhesion points to the membrane, which bias filament bending and constrain membrane height fluctuations, screen the effective attractive interactions between filaments, significantly delaying bundling and tube formation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934920PMC
July 2016

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation.

Proc Natl Acad Sci U S A 2016 Apr 8;113(16):E2224-30. Epub 2016 Mar 8.

Department of Chemistry, University of California, Berkeley, CA 94720.

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1513659113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843481PMC
April 2016

Ligand-Mediated Interactions between Nanoscale Surfaces Depend Sensitively and Nonlinearly on Temperature, Facet Dimensions, and Ligand Coverage.

ACS Nano 2016 Feb 20;10(2):1877-87. Epub 2016 Jan 20.

Department of Chemistry, University of California Berkeley , Berkeley, California 94720, United States.

Nanoparticles are often covered in ligand monolayers, which can undergo a temperature-dependent order-disorder transition that switches the particle-particle interaction from repulsive to attractive in solution. In this work, we examine how changes in the ligand surface coverage and facet dimensions affect the ordering of ligands, the arrangement of nearby solvent molecules, and the interaction between ligand monolayers on different particles. In particular, we consider the case of strongly bound octadecyl ligands on the (100) facet of CdS in the presence of an explicit n-hexane solvent. Depending on the facet dimensions and surface coverage, we observe three distinct ordered states that differ in how the ligands are packed together, and which affect the thickness of the ligand shell and the structure of the ligand-solvent interface. The temperature dependence of the order-disorder transition also broadens and shifts to lower temperature in a nonlinear manner as the nanoscale is approached from above. We find that ligands on nanoscale facets can behave very similarly to those on macroscopic surfaces in solution, and that some facet dimensions affect the ligand alignment more strongly than others. As the ligands order, the interaction between opposing monolayers becomes attractive, even well below full surface coverage. The strength of attraction per unit surface area is strongly affected by ligand coverage, but only weakly by facet width. Conversely, we find that bringing two monolayers together just above the order-disorder transition temperature can induce ordering and attraction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acsnano.5b05569DOI Listing
February 2016

Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step.

J Am Chem Soc 2016 Jan 6;138(2):527-39. Epub 2016 Jan 6.

Physik Department, Technische Universität München , 85748 Garching, Germany.

Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.5b08717DOI Listing
January 2016

Exploiting non-equilibrium phase separation for self-assembly.

Soft Matter 2016 Feb 10;12(5):1517-24. Epub 2015 Dec 10.

Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.

Demixing can occur in systems of two or more particle species that experience different driving forces, e.g., mixtures of self-propelled active particles or of oppositely charged colloids subject to an electric field. Here we show with macroscopic experiments and computer simulations that the forces underlying such non-equilibrium segregation can be used to control the self-assembly of particles that lack attractive interactions. We demonstrate that, depending on the direction, amplitude and frequency of a periodic external force acting on one particle species, the structures formed by a second, undriven species can range from compact clusters to elongated, string-like patterns.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/c5sm01922bDOI Listing
February 2016

Preserving correlations between trajectories for efficient path sampling.

J Chem Phys 2015 Jun;142(23):234104

Department of Chemistry, University of California, Berkeley, California 94720, USA.

Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective on Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this "noise guidance" synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.4922343DOI Listing
June 2015

Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity.

J Phys Chem B 2015 Jun 2;119(23):6963-73. Epub 2015 Jun 2.

∇Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States.

Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.5b03784DOI Listing
June 2015

Fluctuations within folded proteins: implications for thermodynamic and allosteric regulation.

Acc Chem Res 2015 Apr 17;48(4):1098-105. Epub 2015 Feb 17.

§Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.

Folded protein structures are both stable and dynamic. Historically, our clearest window into these structures came from X-ray crystallography, which generally provided a static image of each protein's singular "folded state", highlighting its stability. Deviations away from that crystallographic structure were difficult to quantify, and as a result, their potential functional consequences were often neglected. However, several dynamical and statistical studies now highlight the structural variability that is present within the protein's folded state. Here we review mounting evidence of the importance of these structural rearrangements; both experiment and computation indicate that folded proteins undergo substantial fluctuations that can greatly influence their function. Crucially, recent studies have shown that structural elements of proteins, especially their side-chain degrees of freedom, fluctuate in ways that generate significant conformational heterogeneity. The entropy associated with these motions contributes to the folded structure's thermodynamic stability. In addition, since these fluctuations can shift in response to perturbations such as ligand binding, they may play an important role in the protein's capacity to respond to environmental cues. In one compelling example, the entropy associated with side-chain fluctuations contributes significantly to regulating the binding of calmodulin to a set of peptide ligands. The neglect of fluctuations within proteins' native states was often justified by the dense packing within folded proteins, which has inspired comparisons with crystalline solids. Many liquids, however, can achieve similarly dense packing yet fluidity is maintained through correlated molecular motions. Indeed, the studies we discuss favor comparison of folded proteins not with solids but instead with dense liquids, where the internal side chain fluidity is facilitated by collective motions that are correlated over long distances. These correlated rearrangements can enable allosteric communication between different parts of a protein, through subtle and varied channels. Such long-range correlations appear to be an innate feature of proteins in general, manifest even in molecules lacking known allosteric regulators and arising robustly from the physical nature of their internal environment. Given their ubiquity, it is only to be expected that, over time, nature has refined some subset of these correlated motions and put them to use. Native state fluctuations increasingly appear to be vital for proteins' natural functions. Understanding the diversity, origin, and range of these rearrangements may provide novel routes for rationally manipulating biomolecular activity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ar500351bDOI Listing
April 2015

Heterogeneity-induced large deviations in activity and (in some cases) entropy production.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Oct 15;90(4):042123. Epub 2014 Oct 15.

Department of Chemistry, University of California, Berkeley, California 94720, USA and Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

We solve a simple model that supports a dynamic phase transition and show conditions for the existence of the transition. Using methods of large deviation theory we analytically compute the probability distribution for activity and entropy production rates of the trajectories on a large ring with a single heterogeneous link. The corresponding joint rate function demonstrates two dynamical phases--one localized and the other delocalized, but the marginal rate functions do not always exhibit the underlying transition. Symmetries in dynamic order parameters influence the observation of a transition, such that distributions for certain dynamic order parameters need not reveal an underlying dynamical bistability. Solution of our model system furthermore yields the form of the effective Markov transition matrices that generate dynamics in which the two dynamical phases are at coexistence. We discuss the implications of the transition for the response of bacterial cells to antibiotic treatment, arguing that even simple models of a cell cycle lacking an explicit bistability in configuration space will exhibit a bistability of dynamical phases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.90.042123DOI Listing
October 2014

Communication: Dominance of extreme statistics in a prototype many-body Brownian ratchet.

J Chem Phys 2014 Oct;141(16):161101

Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Many forms of cell motility rely on Brownian ratchet mechanisms that involve multiple stochastic processes. We present a computational and theoretical study of the nonequilibrium statistical dynamics of such a many-body ratchet, in the specific form of a growing polymer gel that pushes a diffusing obstacle. We find that oft-neglected correlations among constituent filaments impact steady-state kinetics and significantly deplete the gel's density within molecular distances of its leading edge. These behaviors are captured quantitatively by a self-consistent theory for extreme fluctuations in filaments' spatial distribution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.4899052DOI Listing
October 2014

Dynamic phase transitions in simple driven kinetic networks.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Jun 5;89(6):062108. Epub 2014 Jun 5.

Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

We analyze the probability distribution for entropy production rates of trajectories evolving on a class of out-of-equilibrium kinetic networks. These networks can serve as simple models for driven dynamical systems, where energy fluxes typically result in nonequilibrium dynamics. By analyzing the fluctuations in the entropy production, we demonstrate the emergence, in a large system size limit, of a dynamic phase transition between two distinct dynamical regimes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.89.062108DOI Listing
June 2014