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A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involved in these processes, and (ii) estimation of the rates or…
Accurately predicting chemical reaction outcomes and potential byproducts is a fundamental task of modern chemistry, enabling the efficient design of synthetic pathways and driving progress in chemical science. Reaction mechanism, which…
The definition of heat in quantum mechanics is ambiguous. Complications arise in particular when the coupling between a quantum system and a thermal environment is non-negligible, as the boundary between the two becomes blurred, making the…
We demonstrate the benefits of a convex geometric perspective for questions on chemical stoichiometry. We show that the balancing of chemical equations, the use of "mixtures" to explain multiple stoichiometry, and the half-reaction for…
In the non-relativistic description of the reaction of composite particles, the reaction matrix is independent of the choice of post or prior forms for the interaction. We generalize this post-prior equivalence to the relativistic reaction…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Heterogeneous gas and solid catalyst reactions occur at the atomic level, and understanding and controlling complex catalytic reactions at this level is crucial for the development of improved processes and materials. There are postulations…
In this paper we demonstrate how asymmetric molecular rotational spectra may be introduced to students both "pictorially" and with simple formulae. It is shown that the interpretation of such spectra relies heavily upon pattern recognition.…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
A novel polar coordinate lattice Boltzmann kinetic model for detonation phenomena is presented and applied to investigate typical implosion and explosion processes. In this model, the change of discrete distribution function due to local…
It is standard in chemistry to represent a sequence of reactions by a single overall reaction, often called a complex reaction in contrast to an elementary reaction. Photosynthesis $6 \text{CO}_2+6 \text{H}_2\text{O} \to \…
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…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
We present a brief overview of nuclear multifragmentation reaction. Basic formalism of canonical thermodynamical model based on equilibrium statistical mechanics is described. This model is used to calculate basic observables of nuclear…
We present a method that captures the fluctuations beyond mean field in chemical reactions in the regime of small copy numbers and hence large fluctuations, using self-consistently determined memory: by integrating information from the past…
The precise control of complex reactions is critical for biological processes yet our inability to design for specific outcomes limits the development of synthetic analogues. Here, we leverage differentiable simulators to design nontrivial…
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…
I propose a novel approach to balancing equations that is applicable to all chemical-reaction equations; it is readily accessible to students via scientific calculators and basic computer spreadsheets that have a matrix-inversion…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…