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We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
This research focuses on the unique phase behavior of non-spherical patchy colloids in porous environments. Based on the theory of scaled particle (SPT), methods have been refined and applied to analyze the thermodynamic properties of…
The parabolic approximation is developed for high energy charged particles scattering in a bent crystal with variable curvature. The general form of parabolic equation is received for atomic chains located along coordinate axis of…
Motivated by observations of heterogeneous domain structure on the surface of cells, we consider a minimal model to describe the dynamics of phase separation on the surface of a spherical particle. Finite-size effects on the curved particle…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Nano- to micro-sized particles with differently charged surface areas exhibit complex interaction patterns, characterized by both opposite-charge attraction and like-charge repulsion. While several successful models have been proposed in…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
The quantum chromodynamics (QCD) phase diagram at large densities and low temperatures can be probed using both neutron stars and low-energy heavy-ion collisions. Heavy-ion collisions are nearly isospin-symmetric systems, whereas neutron…
Particles added to a fluid interface can be used as a surface stabilizer in the food, oil and cosmetic industries. As an alternative to rigid particles, it is promising to consider highly deformable particles that can adapt their…
Colloidal patchy particles with divalent attractive interaction can self-assemble into linear polymer chains. Their equilibrium properties in 2D and 3D are well described by Wertheim's thermodynamic perturbation theory which predicts a…
We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We study the phase structure of a dilute two-component Fermi system with attractive interactions as a function of the coupling and the polarization or number difference between the two components. In weak coupling, a finite number asymmetry…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
We numerically determine the very rich phase diagram of mass-imbalanced binary mixtures of hardcore bosons (or equivalently -- fermions, or hardcore-Bose/Fermi mixtures) loaded in one-dimensional optical lattices. Focusing on commensurate…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…