Erik lindahl professor of biophysics, science for life laboratory, stockholm university verified email at scilifelab. Unraveling the strokes of ion channel molecular machines. View erik lindahl s profile on linkedin, the worlds largest professional community. Stabilization of the glucl ligandgated ion channel in the. Erik lindahls 214 research works with 34733 citations and 7771 reads, including. Biophysics phd program biophysics program stanford medicine. The scientific case for computing in europe 2018 2026. A concept that proposes that individuals pay for the provision of a public good according to their marginal benefits in order to determine the efficient level of provision for. We describe a new tool, called multibody refinement, which models flexible complexes as a userdefined. A drug pocket at the lipid bilayerpotassium channel. In other words, they pay according to the amount of satisfaction or utility they derive from the consumption of an additional unit of the public good it can be seen as an individuals share of the collective tax burden of an economy. Erik lindahls research works kth royal institute of. Professor of biophysics, science for life laboratory, stockholm university.
This cited by count includes citations to the following articles in scholar. Ligandgated ion channels molecular biophysics stockholm. Department of biochemistry and biophysics, science for life laboratory, stockholm university, stockholm, sweden. Erik lindahl on bioresearch advances, the march to mixed. If the chart does not state 2020, the names of this years members will be published later. Swedish escience research center, kth royal institute of technology, stockholm, sweden. Works at department of biochemistry and biophysics. Tackling exascale software challenges in molecular dynamics simulations with gromacs szil. Professor of biophysics department of applied physics. He was professor of economics at uppsala university 194258 and in 195659 he was the president of the international economic association. Department of biochemistry and biophysics, center for biomembrane research, stockholm university, se106 91, stockholm. Professor, computational biophysics, kth royal institute of technology stockholm university.
Here, we present an implementation of the relion image processing. From side chains rattling on picoseconds to ensemble simulations of protein folding. A lindahl tax is a form of taxation conceived by erik lindahl in which individuals pay for public goods according to their marginal benefits. Biophysical journal vol 104, issue 1, pages 1278 8. In a series of seminal contributions, the three laureates provided novel approaches to study complex chemical systems. Molecular dynamics simulations of phospholipid bilayers with. Molecular basis for voltage sensitivity in membrane proteins. Erik lindahl driver helper monarch beverage linkedin. Charmm27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. A half the difference between the two effective defoci resulting from astigmatism. Positionresolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Mar 16, 2018 what is biophysics, applications of biophysics, examples of biophysics,structure of dna, physics concepts.
Implementation of the charmm force field in gromacs. Erik lindahl received a phd from the kth royal institute of technology in 2001, and performed postdoctoral research at groningen university, stanford university and the pasteur institute. Oct 24, 2014 free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. Maps represent the overall structure refined by applying a mask that only covers the protein part without the amphipol belt but with differences in the cytoplasmic cbs domains. The prokaryotic gloeobacter violaceus pentameric ligandgated ion channel glicis an importanttemplatefor studiesofcysloopreceptorsinthe human central nervous system. Human skin barrier structure and function analyzed by cryoem and molecular dynamics. Jun 01, 2018 macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryoem singleparticle analysis. Allosteric potentiation of a ligandgated ion channel is. Electrophysiology of allosteric modulators solna campus af. Theoretical physics, kth royal institute of technology, 10691 stockholm, sweden, 3 utornl center for molecular biophysics, oak ridge national laboratory, 37831 oak ridge, tn, usa, 4 department of biochemistry and cellular and molecular biology. Molecular biophysics department of biochemistry and biophysics our master. We describe a lipidprotein drugbinding pocket of a potassium channel.
Course introduction, repetition of fundamental properties of amino acids, secondary structure in proteins and stabilization. New tools for automated highresolution cryoem structure. Projects in this subgroup combine structure, function, and simulation approaches to characterize various types of pentameric ligandgated ion channels, particularly their modulation by allosteric drugs such as alcohol, anesthetics, or insecticides. They are responsible for a spectrum of key physiological processes in living organisms, including electric signaling and progression along the cell cycle. The biophysics of drug development this collection highlights recent advances in the biophysics of drug development and deliveryareas of central importance to biomedical research.
Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics. Unraveling the strokes of ion channel molecular machines in. Howarda,b, and erik lindahla,b,c,1 adepartment of biochemistry and biophysics, stockholm university, 11419 stockholm, sweden. Bjorn hogberg karolinska institutet department of medical biochemistry and biophysics division of biomaterials and regenerative medicine cosupervisors. The ones marked may be different from the article in the profile. This introductory course on biophysics introduces the principles of electrical excitability of cell membranes, which form the basis of all information processing in the nervous system.
Here, william bialek provides the first graduatelevel introduction to biophysics aimed at physics students. Molecular dynamics simulations of phospholipid bilayers. Curriculum vitae, erik lindahl heidelberg institute for theoretical. Characterisation of molecular motions in cryoem single. Department of theoretical and computational biophysics, maxplanckinstitute of biophysical chemistry, am fassberg 11, d37077 go. The scientific case for computing in europe 2018 2026 the prace scientific steering committee has formulated this third version of the scientific case in relation to a number of areas of major societal relevance, and identified both success stories and breakthroughs that will be possible with investments in next generation infrastructure. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years. Biophysics olle edholm erik lindahl condensed matter physics particle and mathematical physics anders rosengren. A are the azimuthal angles of k and the major astigmatism axis, respectively, c s is the spherical aberration constant of the microscope and. All courses are given by professors who are performing worldclass research. He was an advisor to the swedish government and the central bank. We have here implemented the charmm force field and all necessary extended functional forms in the gromacs molecular simulation package, to make charmmspecific features available and to test them in combination. The program comprises faculty from 16 departments in the.
From side chains rattling on picoseconds to ensemble. Associate professor, computational structural biology. Sep 15, 2014 this special volume focuses on computational molecular biophysics in honor of the 20 nobel prize in chemistry awarded to karplus right, levitt middle, and warshel left. At pracedays in barcelona, hpcwire had the opportunity to interview dr. Mar 25, 2018 course introduction, repetition of fundamental properties of amino acids, secondary structure in proteins and stabilization.
The stanford biophysics program is an interdisciplinary, interdepartmental training program leading to the ph. To date, all molecules targeting known ion channel sites bind to protein pockets that are mainly surrounded by water. Is it possible to get the pdfppt of the lecture read more. For a new generation of physicists, the phenomena of life pose exciting challenges to physics itself, and biophysics has emerged as an important subfield of this discipline. Scheresz1 1mrc laboratory of molecular biology, cambridge, united kingdom 2department of biochemistry and biophysics, science for life laboratory, stockholm university, stockholm, sweden. Erik lindahl, stockholm university biophysics professor and chair of the prace scientific steering committee about the goals of prace, the evolution of pracedays, and the latest bioscience and computing trends. Lindahl posed the question of financing public goods in accordance with individual benefits. Oct 17, 2018 if you want to order paper copies or a printready pdf, please contact the prace communications officer. Automatic gromacs topology generation and comparisons of. Volume 104, issue 1 pages 1278 8 january 20 download full issue. Erik lindahl, professor of biophysics at stockholm university, talks about using the gpuaccelerated gromacs application to simulate protein dynamics. Gromacs is a widely used package for biomolecular simulation, and over the last two decades it has evolved from smallscale efficiency to advanced heterogeneous acceleration and multilevel parallelism targeting some of the largest supercomputers in the world. Many pharmaceutical drugs against neurological and cardiovascular disorders exert their therapeutic effects by binding to specific sites on voltagegated ion channels of neurons or cardiomyocytes.
Biophysical journal vol 114, issue 5, pages e1e2, 1005. Erik and arne have earlier developed research tools such as gromacs, pcons and topcons. In the last century, immense progress has been made to charter and understand a wide range of biological phenomena. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Olle inganas linkopings universitet department of physics, chemistry and biology division of biomolecular and organic electronics ola hermanson. Lindahl mentions they started using cuda in their work nearly five years ago and now 90% of. Johansson, center for biomembrane research and stockholm bioinformatics center, department of biochemistry and biophysics, stockholm university, se10691 stockholm, sweden. Positionsappointments 2009 professor of biophysics, dept. See the complete profile on linkedin and discover erik s.
If you are interested in learning how fundamental biophysics about biological macromolecules such as proteins, dna, and membranes. Biophysics olle edholm erik lindahl condensed matter physics particle and mathematical physics anders rosengren mats wallin tommy ohlsson edwin langmann alexander balatsky patrik henelius. Herman berendsen 20012003 postdoctoral scholar, stanford university school of medicine, usa, michael levitt. Jun 19, 2016 by reaching nearatomic resolution for a wide range of specimens, singleparticle cryoem structure determination is transforming structural biology. Dec 26, 2012 voltagegated ion channels are fascinating micromachines responsible for all electrical signaling in biology. Erik lindahls research works kth royal institute of technology. Molecular dynamics simulations of phospholipid bilayers with cholesterol christofer hofsa, erik lindahl, and olle edholm theoretical biophysics, royal institute of technology, stockholm center for physics, astronomy and biotechnology, se106 91 stockholm, sweden. Erik lindahl 21 november 1891 6 january 1960 was a swedish economist.
Theoretical physics, kth royal institute of technology, 10691 stockholm, sweden, 3 utornl center for molecular biophysics, oak ridge national laboratory, 37831 oak ridge, tn, usa, 4 department of biochemistry and cellular and molecular biology, university of. Positionresolved free energy of solvation for amino acids. He is currently professor of biophysics at stockholm university, with a second appointment as professor of theoretical biophysics. Allosteric potentiation of a ligandgated ion channel is mediated by access to a deep membranefacing cavity stephanie a. Voltagegated ion channels are fascinating micromachines responsible for all electrical signaling in biology. What is biophysics applications of biophysics examples of. Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. Voltagesensitive membrane proteins are united by the ability to transform changes in the membrane potential into mechanical work. Pdf molecular dynamics simulations of phospholipid bilayers. Kth royal institute of technology research at kth leif kari dean school of engineering sciences. Computational modeling of biological membrane and interface. The program centers on understanding biological function in terms of physical and chemical principles. Molecular basis for voltage sensitivity in membrane. Associate editor nathan baker has included a mix of computational and experimental research articles that provide detailed biophysical insight into the.
To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different. Tackling exascale software challenges in molecular. Tackling exascale software challenges in molecular dynamics. Molecular biophysics stockholm is a group of academic and industry researchers and engineers based at the science for life laboratory in solna, stockholm county, sweden group members affiliated with kth royal institute of technology, stockholm university, karolinska institute, and erco pharma conduct computational and complementary structurefunction studies on biomolecules.