Dynamic Pathways for Viral Capsid Assembly

We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile, while for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.Comment: 13 pages, 13 figures. Submitted to Biophys.

Steps and terraces at quasicrystal surfaces. Application of the 6d-polyhedral model to the analysis of STM images of i-AlPdMn

6-d polyhedral models give a periodic description of aperiodic quasicrystals. There are powerful tools to describe their structural surface properties. Basis of the model for icosahedral quasicrystals are given. This description is further used to interpret high resolution STM images of the surface of i-AlPdMn which surface preparation was followed by He diffraction. It is found that both terrace structure and step-terrace height profiles in STM images can be consistently interpreted by the described model

Coarse-grained models for self-assembling systems

In the last years, a considerable deal of work has so far been spent to understand and hence harness the physical principles that underpin the general properties of self-assembling systems. In particular, theoretical and computational modelling have been extensively used to obtain a detailed description of the actual process. This thesis reports on computational work, focusing on two different self-assembling systems and from two distinct perspectives. In the first part, a computational study of the self-assembly of string-like rigid templates in solution aims to explore to what extent it is possible to direct the assembly of the templates into knotted or linked structures by suitably tuning geometrical parameters of the system. The second part is devoted to some of the smallest instances of molecular self-assembly in nature, that is viral capsids. We report on the development of a physics-based algorithm to subdivide the structure of a capsid in quasi-rigid units, helping to elucidate the pathway of assembly from the identification of its building blocks with a top-down approach

Synchrotron X-ray operando studies of atomic structure evolution of multi-component Al alloys in liquid state

This research has studied one of the challenging scientific issues in materials science, i.e., in real time, understanding quantitatively the 3D atomic structures of multiple component alloys in the liquid state and how the atomic structures evolve with temperatures until the onset of crystal nucleation. Four Al-based alloys were used in the research: (1) Al-0.4Sc, (2) Al-1.5Fe, (3) Al-5Cu-1.5Fe and (4) Al-5Cu-1.5Fe-1Si alloy (all in weight percentage). All alloys were heated up to the liquid state and then cooled down with predefined cooling rates using a dedicated solidification apparatus. During cooling, synchrotron X-ray was used to illuminate onto the samples and the total scattering data were collected at the target temperatures. Based on the total scattering data, the empirical potential structure refinement (EPSR) method was used to model and reconstruct the 3D atomic structures in the liquid state at the selected temperatures for each alloy. The research has demonstrated that the EPSR is a computationally efficient tool for searching and finding the solutions of 3D atomic structures according to the measured total scattering data. For the studied alloys, the research reveals fully the temperature-dependent structure heterogeneity and their evolutions with temperature. The key findings of the research are: (1) For the Al-0.4Sc alloy, at the short-range scale in the liquid state, Sc-centred Al polyhedrons form icosahedral type structures with the Al coordination number in the range of 10–12. As the melt is cooled down, the Sc-centred polyhedrons become more compacted, and the connections between adjacent polyhedrons change from more vertex connection to more edge and then more face-sharing connection. At the medium-range scale, the Sccentred clusters with face-sharing are proved to be the “precursors” for the L12 Al3Sc primary phase in the liquid-solid coexisting region. (2) For the three Fe-containing alloys, atomic structural heterogeneities were found to exist in the 1st atomic shell and beyond. The degree of structural heterogeneities is related with the difference in atom radius, atomic bond length and the chemical preference between different atoms in each alloy. The competition resulted in that the Al-centred clusters expand, i.e., with larger bond length, while the solute atom-centred clusters contract, so with the reduced bond length. (3) At the short-range scale, the structural heterogeneities were characterised by the co-existence and growth of the icosahedra-like (ICO-like) and crystal-like structures. During cooling, the Fe atoms show a higher degree of crystallinity than other atoms in the liquids. At the onset of crystal nucleation, relative percentage of the Fe-centred ICO-like and crystal-like Voronoi polyhedrons (VPs) reaches 8-10%, and the others in the range of 5.8-8.5%. (4) The Fe-centred short-range orders (SROs) tend to connect together via five different modes to form larger Fe-centred medium-range orders (MROs). The percentage of the face-sharing increases almost linearly as the temperature is cooled down, approximately 18-20% at the onset of nucleation in the 3 melts. The Fe-centred MROs gradually approach to the structures of the Al13Fe4 primary phase (monoclinic structure) and are proved to be the nucleation precursors for the Al13Fe4 phases. (5) For the quaternary Al-Cu-Fe-Si alloy melt, the research found that the liquid first transfers into a quasicrystal-like, metastable monoclinic Al13Fe4 phase. Such primary phase was confirmed to have a higher degree of five-fold and crystalline symmetry than the liquid. Upon cooling, the Fe-centred five-fold and crystalline symmetry both get enhanced in liquid, leading to a smaller Al13Fe4-liquid configuration entropy difference and interfacial free energy

Making and Breaking of Chemical Bonds: Dynamics of elementary reactions from gas phase to condensed phase

The present thesis is concerned with the dynamics of elementary chemical reactions. In particular, the processes of bond formation (association) and of bond cleavage (dissociation) are studied. Both photo-induced and solvent-induced reaction mechanisms are elucidated. By embedding simple diatomic model systems in rare gas clusters and matrices, the transition of the dynamics of making and breaking of chemical bonds from the gas phase to the condensed phase is systematically investigated

All-Atom Multiscale Computational Modeling Of Viral Dynamics

Thesis (Ph.D.) - Indiana University, Chemistry, 2009Viruses are composed of millions of atoms functioning on supra-nanometer length scales over timescales of milliseconds or greater. In contrast, individual atoms interact on scales of angstroms and femtoseconds. Thus they display dual microscopic/macroscopic characteristics involving processes that span across widely-separated time and length scales. To address this challenge, we introduced automatically generated collective modes and order parameters to capture viral large-scale low-frequency coherent motions. With an all-atom multiscale analysis (AMA) of the Liouville equation, a stochastic (Fokker-Planck or Smoluchowski) equation and equivalent Langevin equations are derived for the order parameters. They are shown to evolve on timescales much larger than the 10^(-14)-second timescale of fast atomistic vibrations and collisions. This justifies a novel multiscale Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX) approach, which propagates viral atomistic and nanoscale dynamics simultaneously by solving the Langevin equations of order parameters implicitly without the need to construct thermal-average forces and friction/diffusion coefficients. In MD/OPX, a set of short replica MD runs with random atomic velocity initializations estimate the ensemble average rate of change in order parameters, extrapolation of which is then used to project the system over long time. The approach was implemented by using NAMD as the MD platform. Application of MD/OPX to cowpea chlorotic mottle virus (CCMV) capsid revealed that its swollen state undergoes significant energy-driven shrinkage in vacuum during 200ns simulation, while for the native state as solvated in a host medium at pH 7.0 and ionic strength I=0.2M, the N-terminal arms of capsid proteins are shown to be highly dynamic and their fast fluctuations trigger global expansion of the capsid. Viral structural transitions associated with both processes are symmetry-breaking involving local initiation and front propagation. MD/OPX accelerates MD for long-time simulation of viruses, as well as other large bionanosystems. By using universal inter-atomic force fields, it is generally applicable to all dynamical nanostructures and avoids the need of parameter recalibration with each new application. With our AMA method and MD/OPX, viral dynamics are predicted from laws of molecular physics via rigorous statistical mechanics