Related papers: A Vector-Based Algorithm for Generating Complete B…
Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a…
In this paper we study how to determine if a linear biochemical network satisfies the detailed balance condition, without knowing the details of all the reactions taking place in the network. To this end, we use the formalism of response…
A lattice of integers is the collection of all linear combinations of a set of vectors for which all entries of the vectors are integers and all coefficients in the linear combinations are also integers. Lattice reduction refers to the…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop…
Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order O(N), where $N$ is the number of particles. The algorithm works very effectively when the particles…
We study the extragradient method for solving vector quasi-equilibrium problems in Banach spaces, which generalizes the extragradient method for vector equilibrium problems and scalar quasi-equilibrium problems. We propose a regularization…
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…
A new method for solving systems of linear algebraic equations of a special type arising in solving problems of image reconstruction has been proposed. This method, due to a certain symmetry of the matrix and the choice of the voxel…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
Chemical laboratory automation has long been constrained by rigid workflows and poor adaptability to the long-tail distribution of experimental tasks. While most automated platforms perform well on a narrow set of standardized procedures,…
We consider a chemical reaction network governed by mass action kinetics and composed of N different species which can reversibly form heterodimers. A fast iterative algorithm is introduced to compute the equilibrium concentrations of such…
Combining the representations of the words that make up a sentence into a cohesive whole is difficult, since it needs to account for the order of words, and to establish how the words present relate to each other. The solution we propose…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
We consider an online vector balancing game where vectors $v_t$, chosen uniformly at random in $\{-1,+1\}^n$, arrive over time and a sign $x_t \in \{-1,+1\}$ must be picked immediately upon the arrival of $v_t$. The goal is to minimize the…