2,000 research outputs found
Quantum Electrodynamics of the Helium Atom
Using singlet S states of the helium atom as an example, I describe precise
calculation of energy levels in few-electron atoms. In particular, a complete
set of effective operators is derived which generates O(m*alpha^6) relativistic
and radiative corrections to the Schr"odinger energy. Average values of these
operators can be calculated using a variational Schr"odinger wave function.Comment: 23 pages, revte
Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification
Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size
Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T 0 ) and liganded (R 4 ) tetramers are stable in solution, the published MD simulations of T 0 undergo a rapid quaternary transition to an R-like structure. We show that T 0 is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T 0 tetramer, to be manifested. Even in the largest box, T 0 is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems
Theory of Anomalous Hall Effect in a Heavy fermion System with a Strong Anisotropic Crystal Field
In a heavy fermion system, there exists the anomalous Hall effect caused by
localized -orbital freedom, in addition to the normal Hall effect due to the
Lorentz force. In 1994, we found that the Hall coefficient caused by the
anomalous Hall effect () is predominant and the relation ( is the electrical resistivity) holds at low
temperatures in many compounds. In this work, we study the system where the
magnetic susceptibility is highly anisotropic due to the strong crystalline
electric field on -orbitals. Interestingly, we find that is
nearly isotropic in general. This tendency is frequently observed
experimentally, which has casted suspicion that the anomalous Hall effect may
be irrelevant in real materials. Our theory corresponds to corrections and
generalizations of the pioneering work on ferromagnetic metals by Karplus and
Luttinger.Comment: 4 pages, revtex, to be published in J. Phys. Soc. Jpn. (No.8
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed
Pokefind: a novel topological filter for use with protein structure prediction
Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein structure prediction methods such as Rosetta. We previously created the Knotfind algorithm, successfully decreasing the frequency of knotted Rosetta models during CASP6. We observed an additional class of knot-like loops that appeared to be equally un-protein-like and yet do not contain a mathematical knot. These topological features are commonly referred to as slip-knots and are caused by the same mechanisms that result in knotted models. Slip-knots are undetectable by the original Knotfind algorithm. We have generalized our algorithm to detect them, and analyzed CASP6 models built using the Rosetta loop modeling method
Sequencing of folding events in Go-like proteins
We have studied folding mechanisms of three small globular proteins: crambin
(CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3)
which are modelled by a Go-like Hamiltonian with the Lennard-Jones
interactions. It is shown that folding is dominated by a well-defined
sequencing of events as determined by establishment of particular contacts. The
order of events depends primarily on the geometry of the native state.
Variations in temperature, coupling strengths and viscosity affect the
sequencing scenarios to a rather small extent. The sequencing is strongly
correlated with the distance of the contacting aminoacids along the sequence.
Thus -helices get established first. Crambin is found to behave like a
single-route folder, whereas in CI2 and SH3 the folding trajectories are more
diversified. The folding scenarios for CI2 and SH3 are consistent with
experimental studies of their transition states.Comment: REVTeX, 12 pages, 11 EPS figures, J. Chem. Phys (in press
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