Tag | Beckstein Lab

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Tag Archives: molecular-dynamics-simulations
Research Experience for Undergraduates (Summer 2017)

Research Experience for Undergraduates (Summer 2017)

The Beckstein Lab offers a fully funded ten-week research program in computational biophysics for a highly motivated undergraduate student. This is a NSF-sponsored Research Experience for Undergraduates (REU). Deadline for applications is May 5, 2017.

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Research Experience for Undergraduates (Summer 2016)

Research Experience for Undergraduates (Summer 2016)

The Beckstein Lab offers a fully funded ten-week research program in computational biophysics for a highly motivated undergraduate student. This is a NSF-sponsored Research Experience for Undergraduates. Deadline for applications is May 30, 2016.

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Molecular basis of ion translocation in sodium/proton antiporters

Molecular basis of ion translocation in sodium/proton antiporters

We studied the process of sodium/proton antiport in the NapA transporter. Through a combination of X-ray crystallography, biochemistry and computer simulations we could show that the antiporter undergoes a large conformational transition that resembles a *elevator*-like movement whereby a single domain moves up- and down through the membrane and carries a sodium ion with it.

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Project: Simulation of transmembrane transport

Project: Simulation of transmembrane transport

A central process in maintaining life is the transport of ions or small molecules such as nutrients across the cell membrane by secondary active transporter proteins. In this project you will use molecular dynamics (MD) computer simulations to study some of the fundamental principles by which transporters act as molecular machines that transduce energy through macromolecular conformational changes. In particular, you will attempt to solve a molecular puzzle : how can a large transported molecule fit through a transporter protein that according to experimental structural data appears too narrow?

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Research Experience for Undergraduates (Summer 2015)

Research Experience for Undergraduates (Summer 2015)

The Beckstein Lab offers a fully funded ten-week research program in computational biophysics for a highly motivated undergraduate student. This is a NSF-sponsored Research Experience for Undergraduates. Deadline for applications is May 31, 2015.

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Tsong Prize for Ian Welland

Tsong Prize for Ian Welland

Undergraduate student Ian Welland was awarded the 2015 Tsong Prize for Undergraduate Research in the Department of Physics at Arizona State University for his work on Quantifying Solvent Kinetics with Kinetic Networks.

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Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights

Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights

A new crystal structure of the Escherichia coli NhaA dimer reveals a previously unidentified salt bridge between two highly conserved residues at the putative binding site. The combination of structural data with molecular dynamics simulations yields new insights into the transport mechanism.

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Molecular mechanism of ligand recognition by the Mhp1 transporter

Molecular mechanism of ligand recognition by the Mhp1 transporter

The hydantoin transporter Mhp1 is a sodium?coupled secondary active transport protein of the nucleobase?cation?symport family and shares the widespread 5?helix inverted repeat transporter architecture. Our previous work showed Mhp1 functions according to the alternating access mechanism. In our new paper in EMBO J , we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site?directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands.

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Summer Book Club 2014: Molecular Simulations and Theory

Summer Book Club 2014: Molecular Simulations and Theory

This summer’s Lab Book Club is designed to provide a thorough review of fundamental concepts for understanding biomolecular simulation and, in particular,molecular dynamics simulations (MD). The material is primarily based on chapters from Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman.

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Ian Kenney

Ian Kenney

Ian Kenney is an undergraduate major in physics. He is working on methods and protocols to accurately calculate solvation energies of small and drug-like molecules and he is also interested in large-scale simulations with millions of particles.

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Sampling macromolecular transitions

Sampling macromolecular transitions

While equilibrium MD is considered the most robust approach to simulating macromolecular conformational changes, conformational transitions are rare events that take place on much faster timescales than the waiting times spent in metastable equilibrium states. Equilibrium simulations thus spend relatively little time sampling actual transition events. Fast transition path sampling methods seek to mitigate the rare event sampling problem, though the full extent to which biased or coarse-grained approaches can replicate physical ensembles of transitions is unknown.

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Project: Predicting protonation states in proteins

Project: Predicting protonation states in proteins

In this rotation project you will predict known and unknown pKa values of key residues in proteins with a new method that combines molecular dynamics simulations with fast heuristic predictions. You will learn to write programs in the Python language and contribute to the open source MDAnalysis library.

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