Related papers: Mathematical Analysis for a Class of Stochastic Co…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
A non-Newtonian flow of a polymer melt is discussed. The description of the exponential decrease of the apparent viscosity by the well-known Eyring formula with an activation energy reduction proportional to the shear stress does not take…
In this paper, we study the problem of transient signal analysis. A signal-dependent algorithm is proposed which sequentially identifies the countable sets of decay rates and expansion coefficients present in a given signal. We…
A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained…
Stochastic hydrodynamics is a central tool in the study of first order phase transitions at a fundamental level. Combined with sophisticated free energy models, e.g. as developed in classical Density Functional Theory, complex processes…
We study statistical copolymerization effects on the upper critical solution temperature (CST) of generic homopolymers by means of coarse-grained Langevin dynamics computer simulations and mean-field theory. Our systematic investigation…
A system of particles is studied in which the stochastic processes are one-particle type-change (or one-particle diffusion) and multi-particle annihilation. It is shown that, if the annihilation rate tends to zero but the initial values of…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…
A biological system consists of a variety of polymers that are synthesized from monomers, by catalysis that exists only for some long polymers. It is important to elucidate the emergence and sustenance of such autocatalytic polymerization.…
We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…
The behaviour of many dynamic real phenomena shows different phases, with each one following a sigmoidal type pattern. This requires studying sigmoidal curves with more than one inflection point. In this work, a diffusion process is…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Within the so-called scaled quantum theory, the standard bouncing ball problem is analyzed under the presence of a gravitational field and harmonic potential. In this framework, the quantum-classical transition of the density matrix is…
We consider stochastic and open quantum systems with a finite number of states, where a stochastic transition between two specific states is monitored by a detector. The long-time counting statistics of the observed realizations of the…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
A geometrically nonlinear continuum mechanical theory is formulated for deformation and failure behaviors of amorphous polymers. The model seeks to capture material response over a range of loading rates, temperatures, and stress states…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
We derive the stochastic master equations, that is to say, quantum filters, and master equations for an arbitrary quantum system probed by a continuous-mode bosonic input field in two types of non-classical states. Specifically, we consider…
We present a theory for the dynamical evolution of a quantum system coupled to a complex many-body intrinsic system/environment. By modelling the intrinsic many-body system with parametric random matrices, we study the types of effective…