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We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
Nonlinear contraction theory is a comparatively recent dynamic control system design tool based on an exact differential analysis of convergence, in essence converting a nonlinear stability problem into a linear time-varying stability…
We constructed a model that evolved from a non-equilibrium state to an equilibrium state. The model only needs two basic coefficients, including self-similar coefficients and non-equilibrium coefficients. The coefficients of the model can…
In this paper we consider the dynamics of harmonically-confined atomic gases. We present various general results which are independent of particle statistics, interatomic interactions and dimensionality. Of particular interest is the…
We investigate phase transitions in the nonequilibrium dynamics of power-law interacting spin-1/2 bilayer XXZ models, which have recently been shown to allow generation of entanglement in the form of two-mode squeezing. We find a transition…
We investigate finite size scaling aspects of disorder reaction-diffusion processes in one dimension utilizing both numerical and analytical approaches. The former averages the spectrum gap of the associated evolution operators by doubling…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
Differential growth processes play a prominent role in shaping leaves and biological tissues. Using both analytical and numerical calculations, we consider the shapes of closed, elastic strips which have been subjected to an inhomogeneous…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
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…
Motivated by the experimental search for the QCD critical point we perform simulations of a stochastic field theory with purely relaxational dynamics (model A). We verify the expected dynamic scaling of correlation functions. Using a finite…
The connection between domain relaxations at individual scales and the collective heterogeneous response in non-equilibrium systems is a topic of profound interest in recent times. In a model sys- tem of constantly driven oppositely charged…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
The development of physical simulators, called Ising machines, that sample from low energy states of the Ising Hamiltonian has the potential to drastically transform our ability to understand and control complex systems. However, most of…
We investigate the large-time scaling regimes arising from a variety of metastable structures in a chain of Ising spins with both first- and second-neighbor couplings while subject to a Kawasaki dynamics. Depending on the ratio and sign of…
A quasistatic model for a horizontally loaded thin elastic composite at small strains is studied. The composite consists of two adjacent plates whose interface behaves in a cohesive fashion with respect to the slip of the two layers. We…
Taking the two-dimensional Ising model for example, short-time behavior of critical dynamics with a conserved order parameter is investigated by Monte Carlo simulations. Scaling behavior is observed, but the dynamic exponent $z$ is updating…
Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes…