Related papers: A Three-State Thermodynamically Consistent Cross-B…
We pose the problem of metastability for a three--state spin system with conservative dynamics. We consider the Blume--Capel model with the Kawasaki dynamics, we prove that, in a particular region of the parameter plane, the metastable…
We present a quantitative analysis of recent data on the kinetics of ATP hydrolysis, which has presented a puzzle regarding the load dependence of the Michaelis constant. Within the framework of coarse grained two-state ratchet models, our…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The Multiscale Entanglement Renormalization Ansatz (MERA) is a tensor network based variational ansatz that is capable of capturing many of the key physical properties of strongly correlated ground states such as criticality and topological…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
We develop a new extended version of the mode-coupling theory (MCT) for glass transition, which incorporates activated hopping processes via the dynamical theory originally formulated to describe diffusion-jump processes in crystals. The…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
Many natural and engineering systems are simultaneously subjected to a driving force and a stabilizing force. The interplay between the two forces, especially for highly nonlinear systems such as fluid flow, often results in surprising…
We revisit here the mathematical model for ATP production in mitochondria introduced recently by Bertram, Pedersen, Luciani, and Sherman (BPLS) as a simplification of the more complete but intricate Magnus and Keizer's model. We identify…
Muscles are biological actuators extensively studied in the frame of Hill's classic empirical model as isolated biomechanical entities, which hardly applies to a living organism subjected to physiological and environmental constraints. Here…
We study the normal state and the superconducting transition in the Attractive Hubbard Model in three dimensions, using self-consistent diagrammatics. Our results for the self-consistent $T$-matrix approximation are consistent with 3D-XY…
Dynamics with a threshold input--output relation commonly exist in gene, signal-transduction, and neural networks. Coupled dynamical systems of such threshold elements are investigated, in an effort to find differentiation of elements…
We consider a gauge theory of the glass transition in the frustrated XY model being simplest model containing topologically nontrivial excitations. We describe the transition kinetics and find that the three-dimensional system exhibits the…
Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even in the presence of oxygen, to the secretion of carbon…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
DNA mismatch repair (MMR) is the essential mechanism for preserving genomic integrity in various living organisms. In this process, MutS homologs (MSH) play crucial roles in identifying mismatched basepairs and recruiting downstream MMR…
We present a mode-coupling theory (MCT) for the high-density dynamics of two-dimensional spherical active Brownian particles (ABP). The theory is based on the integration-through-transients (ITT) formalism and hence provides a starting…
A new generation of experiments on dry macroscopic friction has revealed that the transition from static to dynamic friction is essentially a spatially and temporally non-uniform process, initiated by a rupture-like detachment front. We…
We propose a simple phenomenological model for wet granular media to take into account many particle interaction through liquid in the funicular state as well as two-body cohesive force by a liquid bridge in the pendular state. In the wet…
The pervasive phenomenon of friction has been studied at the nanoscale by controlled manipulation of single atoms and molecules, which permitted a precise determination of the static friction force necessary to initiate motion. However,…