Related papers: Multiple scales and phases in discrete chains with…
We propose an approach to sensitively probe the chirality of molecules by measuring their coherent optical absorption spectra. It is shown that quantum dynamics of the cyclic three-level chiral molecules driven by appropriately-designed…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
Analogous to a model that predicts the linear scaling of the binding energy of a nucleus from the number of nucleons, a simple model was developed to account for the observed linear variation of the quantum-chemically computed total…
Order parameters based on spherical harmonics and Fourier coefficients already play a significant role in condensed matter research in the context of systems of spherical or point particles. Here, we extend these types of order parameter to…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequences alone for the small (40,42 aa) plaque-forming amyloid…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
We study the dynamical properties of the ordered phases obtained in a coupled nonequilibrium system describing advection of two species of particles by a stochastically evolving landscape. The local dynamics of the landscape also gets…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We use a standard bead-spring model and molecular dynamics simulations to study the static properties of symmetric linear multiblock copolymer chains and their blocks under poor solvent conditions in a dilute solution from the regime close…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
The critical incompatibility of polymers with different compositions scales inversely with their length. For instance, a mixture of A and B homopolymers of length $N$ segregates at $\chi_{AB}^{cr} = 2/N$. But what if the difference between…