Related papers: Partial equilibrium approximations in Apoptosis
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
Biological samples continuously emit ultra-weak photon emission (UPE, or "biophotons") which stems from electronic excited states generated chemically during oxidative metabolism and stress. Thus, UPE can potentially serve as a method for…
Partial differential equations (PDEs) are among the most universal and parsimonious descriptions of natural physical laws, capturing a rich variety of phenomenology and multi-scale physics in a compact and symbolic representation. This…
This paper proposes a novel reaction-diffusion system approximation tailored for singular diffusion problems, typified by the fast diffusion equation. While such approximation methods have been successfully applied to degenerate parabolic…
In this paper we present a method for estimating unknown parameter that appear on a non-linear reaction-diffusion model of cancer invasion. This model considers that tumor-induced alteration of micro-enviromental pH provides a mechanism for…
Computational chemistry has become an important tool to predict and understand molecular properties and reactions. Even though recent years have seen a significant growth in new algorithms and computational methods that speed up quantum…
A discrete-time totally asymmetric simple exclusion process on a lattice with open boundaries is considered. There are particles of different types. The type of a particle is characterized by the probability that a particle moves to a…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…
In this paper, a quantitative measure of partial observability is defined for PDEs. The quantity is proved to be consistent if the PDE is approximated using well-posed approximation schemes. A first order approximation of an unobservability…
Parabolic partial differential equations (PDEs) appear in many disciplines to model the evolution of various mathematical objects, such as probability flows, value functions in control theory, and derivative prices in finance. It is often…
The differential cross sections of $pD\to ^3He X$ reactions, where $X=\eta, \ \eta'\ ,\omega, \ \phi $, are calculated on the basis of a two-step mechanism involving the subprocesses $pp\to d\pi ^+$ and $\pi^+n\to Xp $. It is shown that…
The realistic modeling intended to quantify precisely some biological mechanisms is a task requiering a lot of a priori knowledge and generally leading to heavy mathematical models. On the other hand, the structure of the classical Machine…
Dynamical systems describe the changes in processes that arise naturally from their underlying physical principles, such as the laws of motion or the conservation of mass, energy or momentum. These models facilitate a causal explanation for…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
In this paper we find explicit formulas for: (1) Green's function for a system of one-dimensional bosons interacting via a delta-function potential with particles confined to the positive half-line; and (2) the transition probability for…
Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to…
Many biological processes exhibit oscillatory behavior. Among these, glycolytic oscillations have been extensively studied due to their well-characterized biochemical reaction networks. However, the complexity of these networks necessitates…
Efficient approximation lies at the heart of large-scale machine learning problems. In this paper, we propose a novel, robust maximum entropy algorithm, which is capable of dealing with hundreds of moments and allows for computationally…
For a theoretical understanding of the reactivity of complex chemical systems, relative energies of stationary points on potential energy hypersurfaces need to be calculated to high accuracy. Due to the large number of intermediates present…