Department of Physics @ Carnegie Mellon

Theoretical and Computational Biological Physics

 

Part of the Biological Physics Initiative
Carnegie Mellon University, Department of Physics

www.cmu.edu
 
  budding simulation  

news ... news ... news ...

 
 

Cem has defended his thesis!

SABMS logoOn July 2nd 2012 Cem Yolcu successfully defended his thesis on "Effective field theory of surface-mediated forces in soft matter".

We had a lively two hour grilling session in DH 301D, during which the thesis committee (Deserno, Rothstein, Widom, Sekerka, Tilton) probed Cem's understanding of his thesis subject (and managed to get into exciting mutual disagreement among each other, much to the bemusement of Cem). No thermally heated debates ensued, at least not in comparison to the outside temperatures (well, yet another Pittsburgh heat wave). Cem ended up convincing everyone that he knows what he's talking about, not much to anybody's surprise, and we were happy to award him with the honorific he so valiantly worked towards in the past years.

Many congratulations, Cem!

 

 

Tristan has defended his thesis!

SABMS logoOn April 25th 2011 Tristan Bereau successfully defended his thesis on "Unconstrained Structure Formation in Coarse-Grained Protein Simulations".

During an intense two-hour ceremony in Porter Hall 226C, on the only day in this month when temperatures were searing hot indoors, he valiantly defended his manifesto against the relentless batterings of his inquisitorial thesis squad (Deserno, Lösche, Swendsen, Kurnikova, Zuckerman). And try as they might, they were unable to trip him up. They had no choice left and awarded him a "pass" on this day of all days.

Many congratulations, Tristan!

 

 

Biological and Biophysical Basis of Membrane Dynamics and Organization:
A Two-day Workshop at the MI on Nov. 05/06

SABMS logoA large number of scientists in the Pittsburgh region dedicate their research to understanding biological membranes. It is the aim of this workshop to bring us all together, help us to place our research into perspective, strengthen our community, and explore opportunities for collaborations within the Pittsburgh region and beyond.
To learn more about this upcoming event, have a look at the event's webpage.

 

 

 

Multiscale modeling of lipid bilayers under equilibrium and non-equilibrium conditions

SABMS logoThe plasma membrane enveloping mammalian cells is a two-dimensional fluid bilayer consisting primarily of thousands of different types of lipids and proteins. Far from being featureless, it is now well-established that the membrane is "patchy" with spatially organized regions of structure and function, both in terms of lipids and proteins. The spatially-extended nature of the membrane "patchiness" together with dynamic membrane processes, due to both thermodynamic fluctuations and non-equilibrium cellular events (such as endo- and exocytosis), provide challenges for theorists and computational scientists alike to develop and simulate quantitative models that seamlessly "funnel" information via coarse-graining from the molecular length and time scales up to the mesoscale. In this workshop we will address the questions how to systematically coarse-grain the static and dynamic properties of lipid membranes, and how we can efficiently describe the interaction of such membranes with proteins. More information can be found on the webpage of the workshop.

 

 

International Workshop on Self-Assembly in Biology and Materials Science

SABMS logoSelf-Assembly is a phenomenon which is masterfully handled by nature to design many structures of living systems. The same mechanisms can be fruitfully exploited in Materias Science to arrive at materials with novel structures and properties. The aim of this international workshop is to explore this unifying principle from both the point of view of biological physics and engineering and learn more about the deep connections across these disciplines. It will also foster stronger collaborations between Mexican and US scientists working in this field.

The workshop will take place in the hotel Hotel Camino Real Zaashila at the beautiful Pacific beach resort of Huatulco in Oaxaca, México, from June 8–12, 2010. It is organized by Mathias Lösche and Markus Deserno (Carnegie Mellon University), Jaime Ruiz-Garcia (Universidad Autonóma de San Luis Potosí), and Chuck Knobler (UCLA). More information can be found on the webpage of the workshop.

 

 

Tristan Bereau wins Astrid and Bruce McWilliams graduate research fellowship

Bruce McWilliams and Tristan BereauThe Astrid and Bruce McWilliams Fellowship in the Mellon College of Science was established in 2007 by alumnus Bruce McWilliams, chairman of Tessera Technologies’ board of directors and the company’s chief strategy officer; and his wife, Astrid McWilliams. It provides tuition, stipend and fees for up to one year of graduate study, as well as $1000 for conference travel or other research expenses. In 2010 Tristan Bereau has won this fellowship for his continuing successful work on modeling coarse grained peptides (see also his publication in the Journal of Chemical Physics) and studying their thermodynamic and kinetic behavior using state of the art techniques from numerical statistical physics (see his publication in the Journal of Computational Physics).

 

 

International Workshop on Coarse-Grained Biomolecular Modeling

Levi WorkshopOne of the challenging aspects of biomolecular simulations is the vast range of time- and length-scales which must be covered. Coarse grained simulations provide a solution to conquer bigger system and study them for a longer time, but care must be taken that during the process of eliminating degrees of freedom important physics is accidentally eliminated as well. During March 7–12 2010 an International Workshop (a "Winter School") will be held in Levi, Finland, in which such questions will be amply addressed. A special focus will also be on hands-on experiences with current important simulation tools at typical levels of resolution. The focus will be on biomembranes. Lecturers at this school will be Siewert-Jan Marrink (University of Groeningen, the Netherlands), Alex de Vries (University of Groeningen, the Netherlands), Luca Monticelli (INSERM Paris, France), Markus Deserno (Carnegie Mellon University, USA), and Will Noid (Penn State University, USA). Additionally, there will be three invited research talks by Julian Shillcock (MEMPHYS, University of Southern Denmark), Ilpo Vattulainen (Tampere University of Technology, Finland), and Alex Bunker (University of Helsinki, Finland).

Many more details about this event — including instructions for how to apply — can be found on the webpage of this workshop.

 

 

Deserno receives CDI grant from the NSF

membrane-coated nanoparticleThe NSF's CDI program stands for "Cyber-enabled Discovery and Innovation". It's aims are to "explore radically new concepts, approaches and tools at the intersection of computational and physical or biological worlds." Together with Prof. Roland Faller (UC Davis, coordinating PI), Prof. Amadeu Sum (Colorado School of Mines), Prof. Richard Gandour and Prof. Alan Esker (both VirginiaTech) Deserno will explore combined computational and experimental strategies to cyber-engineer functional nanoparticles for targeted drug delivery. Specifically, the Deserno group will use coarse-grained simulations, linked to two finer scales (Faller, Sum) and experiment (Gandour, Esker) to investigate how flat and curved surfaces can be coated with lipid membranes by means of tether molecules. A major aspect of the project, which is funded for 4 years, will also be the development of automated tools for linking simulations at different levels of resolution and experimental data and procedures

 

 

Tristan Bereau wins Guy C. Berry Research Award

Tristan BereauTristan Bereau wins the 2009 Guy C. Berry Graduate Research Award. This award regognizes excellence in research performed by MCS graduate students. It is named after Guy C. Berry, University Professor at Carnegie Mellon, faculty member in the Department of Chemistry, and former Dean of MCS. Tristan receives this award for his development of coarse-grained peptide models and application of state-of-the-art statistical techniques for probing their thermodynamic behavior, also recently published in the Journal of Chemical Physics. Tristan has been a member of the Deserno group from the first hour, when it was established in the fall of 2007. He received his undergraduate degree from the EPFL Lausanne (Switzerland) and had previously visited the Physics Department of Carnegie Mellon during an academic exchange year.

 

 

Headlines

 

On July 2nd 2012 Cem Yolcu successfully defended his thesis! Congratulations, Cem!
On April 25th 2011 Tristan Bereau successfully defended his thesis! Congratulations, Tristan!
Biological and Biophysical Basis of Membrane Dynamics and Organization:
A Two-day Workshop at the MI on Nov. 05/06
International Workshop on Multiscale modeling of lipid bilayers under equilibrium and non-equilibrium conditions
International Workshop on Self-Assembly in Biology and Materials Science
Tristan Bereau wins Astrid and Bruce McWilliams graduate research fellowship.
International Workshop on Coarse-Grained Biomolecular Modeling
Deserno receives CDI grant from NSF
Tristan Bereau wins Guy C. Berry Research Award

Scherk's minimal surface

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twisted torus

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