Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment : from 7th German Conference on Chemoinformatics: 25 CIC-Workshop Goslar, Germany, 6 - 8 November 2011
Florian D. Roessler
Peter J. Bond
- The human immunodeficiency virus (HIV) is currently ranked sixth in the worldwide causes of death . One treatment approach is to inhibit reverse transcriptase (RT), an enzyme essential for reverse transcription of viral RNA into DNA before integration into the host genome . By using non-nucleoside RT inhibitors (NNRTIs) , which target an allosteric binding site, major side effects can be evaded. Unfortunately, high genetic variability of HIV in combination with selection pressure introduced by drug treatment enables the virus to develop resistance against this drug class by developing point mutations. This situation necessitates treatment with alternative NNRTIs that target the particular RT mutants encountered in a patient.
Previously, proteochemometric approaches have demonstrated some success in predicting binding of particular NNRTIs to individual mutants; however a structurebased approach may help to further improve the predictive success of such models. Hence, our aim is to rationalize the experimental activity of known NNRTIs against a variety of RT mutants by combining molecular modeling, long-timescale atomistic molecular dynamics (MD) simulation sampling and ensemble docking. Initial control experiments on known inhibitor-RT mutant complexes using this protocol were successful, and the predictivity for further complexes is currently being evaluated. In addition to predictive power, MD simulations of multiple RT mutants are providing fundamental insight into the dynamics of the allosteric NNRTI binding site which is useful for the design of future inhibitors. Overall, work of this type is hoped to contribute to the development of predictive efficacy models for individual patients, and hence towards personalized HIV treatment options.
Hagedorn states and thermalization : XLIX International Winter Meeting on Nuclear Physics, 24 - 28 January 2011, Bormio, Italy
- In recent years, Hagedorn states have been used to explain the equilibrium and transport properties of a hadron gas close to the QCD critical temperature. These massive resonances are shown to lower h/s to near the AdS/CFT limit close to the phase transition. A comparison of the Hagedorn model to recent lattice results is made and it is found that the hadrons can reach chemical equilibrium almost immediately, well before the chemical freeze-out temperatures found in thermal fits for a hadron gas without Hagedorn states.
Direct photon emission in heavy ion collisions from microscopic transport theory and fluid dynamics : XLVIII International Winter Meeting on Nuclear Physics, BORMIO2010, January 25 - 29, 2010, Bormio, Italy
- Direct photon emission in heavy-ion collisions is calculated within a relativistic micro+macro
hybrid model and compared to the microscopic transport model UrQMD. In the hybrid approach,
the high-density part of the collision is calculated by an ideal 3+1-dimensional hydrodynamic
calculation, while the early (pre-equilibrium-) and late (rescattering-) phase are calculated with
the transport model. Different scenarios of the transition from the macroscopic description to
the transport model description and their effects are studied. The calculations are compared to
measurements by the WA98-collaboration and predictions for the future CBM-experiment are
Implications on the collision dynamics via azimuthal sensitive HBT from UrQMD : the Seventh Workshop on Particle Correlations and Femtoscopy, September 20 - 24 2011, University of Tokyo, Japan
Michael Annan Lisa
- We explore the shape and orientation of the freezeout region of non-central heavy ion collisions.
For this we fit the freezeout distribution with a tilted ellipsoid. The resulting tilt angle is compared
to the same tilt angle extracted via an azimuthally sensitive HBT analysis. This allows to access
the tilt angle experimentally, which is not possible directly from the freezeout distribution. We
also show a systematic study on the system decoupling time dependence on dNch/dh, using HBT
results from the UrQMD transport model. In this study we found that the decoupling time scales
with (dNch/dh)1/3 within each energy, but the scaling is broken across energies.
Strong coupling expansion for Yang-Mills theory at finite temperature
- Euclidean strong coupling expansion of the partition function is applied to lattice Yang-Mills theory
at finite temperature, i.e. for lattices with a compactified temporal direction. The expansions
have a finite radius of convergence and thus are valid only for b <bc, where bc denotes the nearest
singularity of the free energy on the real axis. The accessible temperature range is thus the
confined regime up to the deconfinement transition. We have calculated the first few orders of
these expansions of the free energy density as well as the screening masses for the gauge groups
SU(2) and SU(3). The resulting free energy series can be summed up and corresponds to a glueball
gas of the lowest mass glueballs up to the calculated order. Our result can be used to fix
the lower integration constant for Monte Carlo calculations of the thermodynamic pressure via
the integral method, and shows from first principles that in the confined phase this constant is
indeed exponentially small. Similarly, our results also explain the weak temperature dependence
of glueball screening masses below Tc, as observed in Monte Carlo simulations. Possibilities and
difficulties in extracting bc from the series are discussed.
Towards corrections to the strong coupling limit of staggered lattice QCD : the XXIX International Symposium on Lattice Field Theory - Lattice 2011, July 10 - 16, 2011, Squaw Valley, Lake Tahoe, California
Philippe de Forcrand
- We report on the first steps of an ongoing project to add gauge observables and gauge corrections
to the well-studied strong coupling limit of staggered lattice QCD, which has been shown earlier
to be amenable to numerical simulations by the worm algorithm in the chiral limit and at finite
density. Here we show how to evaluate the expectation value of the Polyakov loop in the framework
of the strong coupling limit at finite temperature, allowing to study confinement properties
along with those of chiral symmetry breaking. We find the Polyakov loop to rise smoothly, thus
signalling deconfinement. The non-analytic nature of the chiral phase transition is reflected in the
derivative of the Polyakov loop. We also discuss how to construct an effective theory for non-zero
lattice coupling, which is valid to O(b).
Screened perturbation theory for 3d Yang-Mills theory and the magnetic modes of hot QCD : International Workshop on QCD Green’s Functions, Confinement, and Phenomenology - QCD-TNT09, September 07 - 11 2009, ECT Trento, Italy
- Perturbation theory for non-abelian gauge theories at finite temperature is plagued by infrared
divergences which are caused by magnetic soft modes ~ g2T, corresponding to gluon fields of
a 3d Yang-Mills theory. While the divergences can be regulated by a dynamically generated
magnetic mass on that scale, the gauge coupling drops out of the effective expansion parameter
requiring summation of all loop orders for the calculation of observables. Some gauge invariant
possibilities to implement such infrared-safe resummations are reviewed. We use a scheme based
on the non-linear sigma model to estimate some of the contributions ~ g6 of the soft magnetic
modes to the QCD pressure through two loops. The NLO contribution amounts to ~ 10% of the
LO, suggestive of a reasonable convergence of the series.
Lattice calculations at non-zero chemical potential: the QCD phase diagram
- The so-called sign problem of lattice QCD prohibits Monte Carlo simulations at finite baryon
density by means of importance sampling. Over the last few years, methods have been developed
which are able to circumvent this problem as long as the quark chemical potential is m=T <~1.
After a brief review of these methods, their application to a first principles determination of the
QCD phase diagram for small baryon densities is summarised. The location and curvature of the
pseudo-critical line of the quark hardon transition is under control and extrapolations to physical
quark masses and the continuum are feasible in the near future. No definite conclusions can as
yet be drawn regarding the existence of a critical end point, which turns out to be extremely quark
mass and cut-off sensitive. Investigations with different methods on coarse lattices show the lightmass
chiral phase transition to weaken when a chemical potential is switched on. If persisting on
finer lattices, this would imply that there is no chiral critical point or phase transition for physical
QCD. Any critical structure would then be related to physics other than chiral symmetry breaking.
Towards a determination of the chiral critical surface of QCD
- The chiral critical surface is a surface of second order phase transitions bounding the region of
first order chiral phase transitions for small quark masses in the fmu;d;ms;mg parameter space.
The potential critical endpoint of the QCD (T;m)-phase diagram is widely expected to be part of
this surface. Since for m = 0 with physical quark masses QCD is known to exhibit an analytic
crossover, this expectation requires the region of chiral transitions to expand with m for a chiral
critical endpoint to exist. Instead, on coarse Nt = 4 lattices, we find the area of chiral transitions
to shrink with m, which excludes a chiral critical point for QCD at moderate chemical potentials
mB < 500 MeV. First results on finer Nt = 6 lattices indicate a curvature of the critical surface
consistent with zero and unchanged conclusions. We also comment on the interplay of phase
diagrams between the Nf = 2 and Nf = 2+1 theories and its consequences for physical QCD.
The finite-temperature phase structure of lattice QCD with twisted-mass Wilson fermions
Maria Paola Lombardo
- We report progress in our exploration of the finite-temperature phase structure of two-flavour lattice
QCD with twisted-mass Wilson fermions and a tree-level Symanzik-improved gauge action
for a temporal lattice size Nt = 8. Extending our investigations to a wider region of parameter
space we gain a global view of the rich phase structure. We identify the finite temperature transition/
crossover for a non-vanishing twisted-mass parameter in the neighbourhood of the zerotemperature
critical line at sufficiently high b . Our findings are consistent with Creutz’s conjecture
of a conical shape of the finite temperature transition surface. Comparing with NLO lattice
cPT we achieve an improved understanding of this shape.