Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate ...irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
2.
Mechanisms of Virus Assembly Perlmutter, Jason D; Hagan, Michael F
Annual review of physical chemistry,
04/2015, Letnik:
66, Številka:
1
Journal Article
Recenzirano
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Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid and in some cases are surrounded by a lipid bilayer membrane. This review summarizes the ...physics that govern the processes by which capsids assemble within their host cells and in vitro. We describe the thermodynamics and kinetics for the assembly of protein subunits into icosahedral capsid shells and how these are modified in cases in which the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques used to characterize capsid assembly, and we highlight aspects of virus assembly that are likely to receive significant attention in the near future.
We examine a minimal model for an active colloidal fluid in the form of self-propelled Brownian spheres that interact purely through excluded volume with no aligning interaction. Using simulations ...and analytic modeling, we quantify the phase diagram and separation kinetics. We show that this nonequilibrium active system undergoes an analog of an equilibrium continuous phase transition, with a binodal curve beneath which the system separates into dense and dilute phases whose concentrations depend only on activity. The dense phase is a unique material that we call an active solid, which exhibits the structural signatures of a crystalline solid near the crystal-hexatic transition point, and anomalous dynamics including superdiffusive motion on intermediate time scales.
We develop a statistical theory for the dynamics of non-aligning, non-interacting self-propelled particles confined in a convex box in two dimensions. We find that when the size of the box is small ...compared to the persistence length of a particle's trajectory (strong confinement), the steady-state density is zero in the bulk and proportional to the local curvature on the boundary. Conversely, the theory may be used to construct the box shape that yields any desired density distribution on the boundary, thus offering a general tool to understand and design such confinements. When the curvature variations are small, we also predict the distribution of orientations at the boundary and the exponential decay of pressure as a function of box size recently observed in simulations in a spherical box.
Confinement of active particles dramatically alters their spatial distribution and mechanical properties.
The study of liquid crystals at equilibrium has led to fundamental insights into the nature of ordered materials, as well as to practical applications such as display technologies. Active nematics ...are a fundamentally different class of liquid crystals, driven away from equilibrium by the autonomous motion of their constituent rod-like particles. This internally generated activity powers the continuous creation and annihilation of topological defects, which leads to complex streaming flows whose chaotic dynamics seem to destroy long-range order. Here, we study these dynamics in experimental and computational realizations of active nematics. By tracking thousands of defects over centimetre-scale distances in microtubule-based active nematics, we identify a non-equilibrium phase characterized by a system-spanning orientational order of defects. This emergent order persists over hours despite defect lifetimes of only seconds. Similar dynamical structures are observed in coarse-grained simulations, suggesting that defect-ordered phases are a generic feature of active nematics.
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment ...assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform dynamical simulations of shell assembly in the presence and absence of cargo over a range of interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell relative to its intrinsic spontaneous curvature, as seen in recent experiments. These features are controlled by a balance of kinetic and thermodynamic effects, and the shell size is assembly pathway dependent. We discuss implications of these results for synthetic biology efforts to target new enzymes to microcompartment interiors.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Optimal Control of Active Nematics Norton, Michael M.; Grover, Piyush; Hagan, Michael F. ...
Physical review letters,
10/2020, Letnik:
125, Številka:
17
Journal Article
Recenzirano
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In this work we present the first systematic framework to sculpt active nematic systems, using optimal control theory and a hydrodynamic model of active nematics. We demonstrate the use of two ...different control fields, (i) applied vorticity and (ii) activity strength, to shape the dynamics of an extensile active nematic that is confined to a disk. In the absence of control inputs, the system exhibits two attractors, clockwise and counterclockwise circulating states characterized by two co-rotating topological +1/2 defects. We specifically seek spatiotemporal inputs that switch the system from one attractor to the other; we also examine phase-shifting perturbations. We identify control inputs by optimizing a penalty functional with three contributions: total control effort, spatial gradients in the control, and deviations from the desired trajectory. This work demonstrates that optimal control theory can be used to calculate nontrivial inputs capable of restructuring active nematics in a manner that is economical, smooth, and rapid, and therefore will serve as a guide to experimental efforts to control active matter.
Autonomous active, elastic filaments that interact with each other to achieve cooperation and synchrony underlie many critical functions in biology. The mechanisms underlying this collective response ...and the essential ingredients for stable synchronization remain a mystery. Inspired by how these biological entities integrate elasticity with molecular motor activity to generate sustained oscillations, a number of synthetic active filament systems have been developed that mimic oscillations of these biological active filaments. Here, we describe the collective dynamics and stable spatiotemporal patterns that emerge in such biomimetic multi-filament arrays, under conditions where steric interactions may impact or dominate the collective dynamics. To focus on the role of steric interactions, we study the system using Brownian dynamics, without considering long-ranged hydrodynamic interactions. The simulations treat each filament as a connected chain of self-propelling colloids. We demonstrate that short-range steric inter-filament interactions and filament roughness are sufficient - even in the absence of inter-filament hydrodynamic interactions - to generate a rich variety of collective spatiotemporal oscillatory, traveling and static patterns. We first analyze the collective dynamics of two- and three-filament clusters and identify parameter ranges in which steric interactions lead to synchronized oscillations and strongly occluded states. Generalizing these results to large one-dimensional arrays, we find rich emergent behaviors, including traveling metachronal waves, and modulated wavetrains that are controlled by the interplay between the array geometry, filament activity, and filament elasticity. Interestingly, the existence of metachronal waves is non-monotonic with respect to the inter-filament spacing. We also find that the degree of filament roughness significantly affects the dynamics - specifically, filament roughness generates a locking-mechanism that transforms traveling wave patterns into statically stuck and jammed configurations. Taken together, simulations suggest that short-ranged steric inter-filament interactions could combine with complementary hydrodynamic interactions to control the development and regulation of oscillatory collective patterns. Furthermore, roughness and steric interactions may be critical to the development of jammed spatially periodic states; a spatiotemporal feature not observed in purely hydrodynamically interacting systems.
Arrays of clamped active filaments, interacting
via
steric forces, display traveling waves and jammed clusters.
Crystallization is fundamental to materials science and is central to a variety of applications, ranging from the fabrication of silicon wafers for microelectronics to the determination of protein ...structures. The basic picture is that a crystal nucleates from a homogeneous fluid by a spontaneous fluctuation that kicks the system over a single free-energy barrier. However, it is becoming apparent that nucleation is often more complicated than this simple picture and, instead, can proceed via multiple transformations of metastable structures along the pathway to the thermodynamic minimum. In this article, we observe, characterize, and model crystallization pathways using DNA-coated colloids. We use optical microscopy to investigate the crystallization of a binary colloidal mixture with single-particle resolution. We observe classical one-step pathways and nonclassical two-step pathways that proceed via a solid–solid transformation of a crystal intermediate. We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments and show that both one- and two-step pathways are driven by thermodynamics alone. Specifically, the two-step solid–solid transition is governed by a competition between two different crystal phases with free energies that depend on the crystal size. These results extend our understanding of available pathways to crystallization, by showing that size-dependent thermodynamic forces can produce pathways with multiple crystal phases that interconvert without free-energy barriers and could provide approaches to controlling the self-assembly of materials made from colloids.
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered ...multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of
, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories:
and
. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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