Computational Physical Chemistry

A central focus of the laboratory’s research interests is the deeper understanding of the macroscopically observed physicochemical and dynamic properties of complex physicochemical and biological processes and systems, with an emphasis on elucidating the molecular mechanisms that give rise to these macroscopic phenomena.
Particular emphasis is placed on predicting the macroscopic properties of matter starting from the molecular level, using molecular simulation, equations of state, and statistical mechanics. The goal is to understand and connect the chemical composition and molecular structure of matter with its macroscopic behavior, ultimately enabling the design of materials and processes based on molecular structure. Within this framework, the lab carries out research that begins with fundamental studies on the principles of statistical thermodynamics and extends to the development of applied thermodynamic models suitable for practical use in process design. A characteristic example of basic research is the proposal for a geometric (Euclidean) description of classical statistical mechanics for systems both in and out of thermodynamic equilibrium. This approach aspires to pave the way for improved descriptions of irreversible processes, both in physical and biological systems.
Special attention has also been given to the creation of innovative techniques, such as the method of Markov chain integration. This method is based on first principles of statistics and enables local “stochastic” integration in combination with the generation of a Markov chain. More generally, the development of a series of prototype methods has often arisen from necessity, but in many cases has led to a deeper understanding of the molecular mechanisms connecting the microscopic and macroscopic worlds.
Notable examples include:
a) Studies on the miscibility of materials and particularly the hydrophobic effect, through the development of methodologies for computing the chemical potential via particle deletion.
b) Modeling of short-range interactions in processes related to protein separation conditions.
c) Sub-glassy relaxation mechanisms in glassy polystyrene, through the development of methods capable of tracking the dynamic evolution of polystyrene on the atomic scale across more than ten orders of magnitude in time. This also includes the development of a prototype probabilistic theory in which both statistics and statistical mechanics are described in a unified Euclidean space shared by probabilities and measurable properties.
Additionally, significant effort has been devoted to developing prototype methods for calculating the total free energy of a system by gradually removing all molecules. Using first-principles tools from statistical mechanics, the chemical work associated with the virtual insertion or deletion of a molecule is computed from stochastic representations of the phase space of both the reference and perturbed systems, offering new applications for perturbation theory.
Finally, beyond the development of prototype statistical mechanics methodologies, in recent years the laboratory has been developing a suite of computational tools based on statistics, geometry, linear system solving, and differential equations. These aim to support the study of:
The transmission of genetic information through the lens of algebra, implementing ideas from Shannon Algebra and the pioneering work of Claude Shannon.
The design and creation of biological analogs of digital information processing systems, using networks of enzymatic reactions to implement logic operations, dynamic memory storage, and biological analogs of basic electronic components.
The study of drug binding to protein targets, by developing computational tools to measure accessible surface areas during drug–protein binding processes.
Beyond the development of prototype methodologies in basic research, a number of tools have also been developed to support the design of physicochemical processes at the level of applied research, particularly concerning the transport and storage of CO₂ and NH₃.