Related papers: Understanding Reaction Mechanisms from Start to Fi…
We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve…
Reaction rates are a complicated function of molecular interactions, which can be selected from vast chemical design spaces. Seeking the design that optimizes a rate is a particularly challenging problem since the rate calculation for any…
Background: Nuclear reactions are complex, with a large number of possible channels. Understanding how different channels contribute to a given reaction is investigated by perturbing the continuous spectrum. Purpose: To develop tools to…
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible…
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…
The Adaptive Multilevel Splitting algorithm is a very powerful and versatile iterative method to estimate the probability of rare events, based on an interacting particle systems. In an other article, in a so-called idealized setting, the…
This chapter aims at emphasizing the crucial role of partial reactivity of a catalytic surface or a target molecule in diffusion-controlled reactions. We discuss various microscopic mechanisms that lead to imperfect reactions, the Robin…
Accurate quantum mechanical treatment of molecular reactions remains a longstanding challenge, especially for reactions involving deep potential wells and long-lived intermediate complexes. Here, we introduce an interaction region…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
Rare event sampling algorithms are essential for understanding processes that occur infrequently on the molecular scale, yet they are important for the long-time dynamics of complex molecular systems. One of these algorithms, transition…
Reaction systems are discrete dynamical systems that model biochemical processes in living cells using finite sets of reactants, inhibitors, and products. We investigate the computational complexity of a comprehensive set of problems…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
The work is presented, leading to the universal contact molecular mechanism of phase transitions and other reactions in solid state. The two components of the mechanism - nucleation and interface propagation - are investigated in detail and…
A key step in the origin of life is the emergence of a primitive metabolism. This requires the formation of a subset of chemical reactions that is both self-sustaining and collectively autocatalytic. A generic theory to study such processes…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…