Carlos Xavier Hernández is a PhD student in the Biophysics Program at Stanford University. He works with Vijay Pande, studying the molecular evolution of proteins and how it affects their structure, dynamics, and function.

Carlos graduated from Columbia University, where he majored in Applied Mathematics. There, he worked with Raul Rabadan and Stephen Goff studying RNA viruses. He has also spent time investigating chemokine receptors with J. Andrew McCammon at UCSD.

Protein Evolution###

Sequence gives rise to function. However, it has become increasingly clear that proteins with wildly different primary structures can yield quite homologous secondary and tertiary structures. For this reason, it is not enough to determine functional residues from just sequence conservation alone. To push forward, novel techniques in bioinformatics, such as statistical coupling analysis, are needed to identify evolved binding sites and protein-protein interfaces. Targeting of such sites could lead to novel drugs that not only fight diseases but whose efficacy is unaffected by mutation of the target protein—a common problem with antivirals.

Molecular Dynamics###

Molecules are small. Too small to be observed directly, in fact. In order to overcome this, Molecular Dynamics (MD) can be used to computationally model whole systems of molecules, like proteins, in atomistic detail. These models can quantify the time-dependent dynamics of molecules and be used to sample the free energy landscape of a system. In doing so, MD simulations can provide insights into the imperceptible mechanisms of protein dynamics and predict experimental observations.

Markov State Models###

Markov state models (MSMs) are a powerful means of modeling the structure and dynamics of molecular systems, like proteins. An MSM is essentially a map of the conformational space a molecule explores. Such models consist of a set of states and a matrix of transition probabilities between each pair of states. These states can be thought of as local minima in the free energy landscape that ultimately determines a molecule’s structure and dynamics. MSMs enable researchers to identify key conformational states and can potentially improve rational drug design.

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    Pandemic Flu Risk Raised by Lax Hog-Farm Surveillance, Wired Science


    The Origin and Evolution of a Pandemic Virus, MAGNet Newsletter, 4:15-18