Statistical Thermodynamics & Molecular Simulations (STMS) Seminar Series
These seminar series are aimed at providing a virtual platform for sharing scientific research in the area of statistical mechanics, molecular simulations, and computational materials science. In recent months, the coronavirus pandemic has stopped all large in-person scientific gatherings, including conferences and department seminars, and it is not clear that the situation will improve any time soon. STMS is aimed at filling this gap, and provide a venue for dissemination of research findings and exchange of ideas in the age of COVID. This model is being currently used by several other scientific communities, and can potentially continue even beyond the pandemic if successful.
Each seminar will be a 60-minute event and will comprise of a long-form (30-minute) talk by a principal investigator or a senior research scientists from academia or industry and a short-form (15-minute) presentation by a graduate student or a postdoc. The remainder of the event will be dedicated to Q&A (10 minutes for the PI, 5 minutes for the student/postdoc). Long-form speakers will be chosen by the STMS Organizing Committee, while we encourage suggestions from the community at large. Student and postdoctoral speakers, however, need to be nominated by their advisors. Seminars will take place on Fridays, from 11 AM-12 PM. During 2021, we expect to hold two seminar per month, at the last two Fridays of each month.This event's talks:
Using computer simulations to advance our understanding of biological systems at the atomic level
Prof. Benoit Roux (University of Chicago)
Abstract: Classical molecular dynamics (MD) simulations based on atomic models play an increasingly important role in a wide range of applications in physics, biology and chemistry. The approach consists of constructing detailed atomic models of the macromolecular system and, having described the microscopic forces with a potential function, using Newton's classical equation, F=ma, to literally "simulate" the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is impossible to access experimentally. While great progress has been made, producing genuine knowledge about biological systems using MD simulations remains enormously challenging. Among the most difficult problems is the characterization of large conformational transitions occurring over long timescales. Issues of force field accuracy, the neglect of induced polarization in particular, are also a constant concern. A powerful paradigm for mapping the conformational landscape of biomolecular systems is to combine free energy methods, transition pathway techniques and stochastic Markov State Model based massively distributed simulations. These concepts will be illustrated with a few recent computational studies of Src tyrosine kinases, K+ channels, and the P-type ion pumps.
Speaker Bio: Benoit Roux was born in the city of Montreal, Canada, in 1958. In 1981, he received a B.Sc. in Physics from the University of Montreal, followed by a M.Sc. in Biophysics in 1985 under the supervision of Remy Sauve. In 1990, he obtained a Ph.D. in Biophysics from Harvard University under the direction of Martin Karplus. He has previously held positions in the Physics Department at the University of Montreal and in the Biophysics Department at the Weill Medical College of Cornell University. Since 2005, he has been at the University of Chicago where he is the Amgen Professor of Biochemistry and Molecular Biology and Professor in the Chemistry Department. Also, he currently holds a joint appointment at Argonne National Laboratory where he is Senior Computational Biologist. An important focus of his laboratory is the understanding of the structure and function of ion channels. We are particularly interested in issues about ion permeation, ion selectivity, gating, and channel inhibitors. He also has a considerable effort aimed at understanding the microscopic factors regulating Src family of tyrosine kinases that play a critical role in the onset of cancer. His research on tyrosine kinases encompasses a combination of experimental and computational approaches to achieve a more complete understanding of Src activation. He is one of the developers of the programs CHARMM and NAMD, and a co-developer of the polarizable Drude force field in collaboration with Alex MacKerell from University of Maryland. In 1998, he was awarded the Rutherford Medal from The Royal Society of Canada and the Noranda Lecture Award from The Chemical Institute of Canada for his work. He was elected Fellow of the Biophysical Society in 2013, and Fellow and National Lecturer Biophysical Society of Canada in 2016.
Extrema in kinetic and thermodynamic variables in the process of ice formation
Mr. Pablo Montero de Hijes (Complutense University of Madrid, Spain)
ABstract: One way ice can form is by growing after homogeneous ice nucleation within supercooled water. In each stage of this process, we may encounter several extreme values in different properties of water. In this talk, I present our results obtained from molecular simulations focused on some of these extrema that occur during ice formation. First, we study the extreme values in two dynamic properties of supercooled water -- viscosity and the self-diffusion coefficient (Montero de Hijes et al. JCP, 149, 094503, 2018). We then focus on to the nucleation stage of ice formation. We studied the extreme values in the nucleation of ice at negative pressures (Bianco et al. PRL, 126, 015704, 2021). Lastly, I will discuss our results on the maximum observed in the growth rate of ice (Montero de Hijes et al. JCP 151 (4) 044509 2019).
Speaker Bio: Pablo Montero de Hijes received his BSc in Physics (2016) and MSc in Chemistry (2017) from Universidad Complutense de Madrid (Spain). During that period, he benefitted from an Erasmus exchange (2014-2015) at Lunds Universitet (Sweden). He also completed internships in the aerospace industry (AIRBUS) and on teaching at the secondary level. In his bachelor’s project, he was introduced to molecular simulations of glasses by his supervisors C Valeriani and E Sanz. After that, he joined Gerhard Gompper’s group for a summer-project on simulations of microswimmers. During his Masters’ he continued studying glasses using molecular simulations with E Sanz and C Valeriani. He is currently pursuing his PhD in Theoretical Chemistry and Computational Modelling at Universidad Complutense de Madrid (Spain) with C Vega and E Sanz. His PhD research has focused on the kinetics and thermodynamics of phase transitions. He has already published nine papers on topics including glass devitrification, supercooled water, nucleation, and ice growth.