BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Penn Engineering Events - ECPv6.16.3//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-WR-CALNAME:Penn Engineering Events
X-ORIGINAL-URL:https://seasevents.nmsdev7.com
X-WR-CALDESC:Events for Penn Engineering Events
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:America/New_York
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20240310T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20241103T060000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20250309T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20251102T060000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20260308T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20261101T060000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20250221T140000
DTEND;TZID=America/New_York:20250221T150000
DTSTAMP:20260602T152010
CREATED:20250130T152631Z
LAST-MODIFIED:20250130T152631Z
UID:13045-1740146400-1740150000@seasevents.nmsdev7.com
SUMMARY:PICS Colloquium: Unraveling Internal Friction in a Coarse-Grained Protein Model
DESCRIPTION:Understanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads\, whose stochastic dynamics can be derived using the Mori-Zwanzig formalism\, capturing both reversible and irreversible interactions. In liquid\, the dissipative bead-bead interactions have so far been restricted to hydrodynamic couplings. However\, friction does not only arises from the solvent but notably\, from the internal degrees of freedom missing in the CG beads. This leads to an additional “internal friction” whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD)\, we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a coarse-grained (CG) model\, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically\, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities\, such as the radial distribution function and the time correlation of bead velocities\, match the corresponding MD values.
URL:https://seasevents.nmsdev7.com/event/13045/
LOCATION:PICS Conference Room 534 – A Wing \, 5th Floor\, 3401 Walnut Street\, Philadelphia\, PA\, 19104\, United States
CATEGORIES:Colloquium
ATTACH;FMTTYPE=image/jpeg:https://seasevents.nmsdev7.com/wp-content/uploads/2025/01/pep-espanol1.jpg
ORGANIZER;CN="Penn Institute for Computational Science (PICS)":MAILTO:dkparks@seas.upenn.edu
END:VEVENT
END:VCALENDAR