Biomedical subjects

Jerome K Percus

Publications and source records attributed to Jerome K Percus.

7 recordsLinked to original sources

PubMed2006

Simple Hamiltonians which exhibit drastic failures by variational determination of the two-particle reduced density matrix with some well known N-representability conditions.

Calculations on small molecular systems indicate that the variational approach employing the two-particle reduced density matrix (2-RDM) as the basic unknown and applying the P, Q, G, T1, and T2 representability conditions provides an accuracy that is competitive with the best standard ab initio methods of quantum chemistry. However, in this paper we consider a simple class of Hamiltonians for which an exact ground state wave function can be written as a single Slater determinant and yet the same 2-RDM approach gives a drastically nonrepresentable result. This shows the need for stronger representability conditions than the mentioned ones.

Journal Article↗

PubMed2005

Size-asymmetric primitive model at low temperature: description of ion pairing and location of the critical point.

We argue that Bjerrum's approach to ion pairing is inappropriate for the size-asymmetric primitive model in the neighborhood of its critical point, and propose a new approach based on the Stillinger-Lovett pairing procedure. The new approach recursively scales up the ion size until linear approximations are suitable for analyzing such a model. To locate the critical point, a residual van der Waals interaction between pairs is added, with an energy cutoff adjusted to match the critical temperature of the restricted primitive model. The locations and downward trends of T(c) and rho(c) with asymmetry are found to compare favorably with simulations.

Journal Article↗

PubMed2005

Duration of an intermittent episode of viremia.

HIV-1 infected patients after being treated with potent combinations of antiretroviral drugs for 2-6 months typically reach a state in which virus can no longer be detected within their blood. These patients with undetectable virus occasionally have viral load measurements that are above the limit of detection of current assays. Such measurements are called blips. Here we examine the possibility that such blips represent infrequent measurements taken during a period of time in which there is a transient elevation of virus in the patient's blood, i.e., a so-called transient episode of viremia. By analyzing time series of blips from a large number of patients, we conclude that transient episodes of viremia exist and that on average they extend for a period of about 3 weeks.

Anti-HIV Agents↗

PubMed2005

Small population effects in stochastic population dynamics.

The discreteness of units of small populations can produce large fluctuations from a classical continuous representation, especially when null populations play a crucial role. These belong to what are here referred to as emergent and evanescent species. A few model biological systems are introduced in which this is the case, as well as a toy model that suggests a path to avoid the associated mathematical complexities. The corresponding division into null and non-null population sectors is carried out to leading order for the model systems, with promising results.

Ecosystem↗

PubMed2004

The reduced density matrix method for electronic structure calculations and the role of three-index representability conditions.

The variational approach for electronic structure based on the two-body reduced density matrix is studied, incorporating two representability conditions beyond the previously used P, Q, and G conditions. The additional conditions (called T1 and T2 here) are implicit in the work of Erdahl [Int. J. Quantum Chem. 13, 697 (1978)] and extend the well-known three-index diagonal conditions also known as the Weinhold-Wilson inequalities. The resulting optimization problem is a semidefinite program, a convex optimization problem for which computational methods have greatly advanced during the past decade. Formulating the reduced density matrix computation using the standard dual formulation of semidefinite programming, as opposed to the primal one, results in substantial computational savings and makes it possible to study larger systems than was done previously. Calculations of the ground state energy and the dipole moment are reported for 47 different systems, in each case using an STO-6G basis set and comparing with Hartree-Fock, singly and doubly substituted configuration interaction, Brueckner doubles (with triples), coupled cluster singles and doubles with perturbational treatment of triples, and full configuration interaction calculations. It is found that the use of the T1 and T2 conditions gives a significant improvement over just the P, Q, and G conditions, and provides in all cases that we have studied more accurate results than the other mentioned approximations.

Journal Article↗

PubMed2003

The distribution of viral blips observed in HIV-1 infected patients treated with combination antiretroviral therapy.

Human immunodeficiency virus type 1 (HIV-1) infected patients treated with combination antiretroviral therapy frequently have the level of HIV-1 RNA detectable in plasma driven below the lower limit of detection of current assays, 50 copies ml(-1). Patients may continue to exhibit viral loads (VLs) below the assay limit for years, yet on some occasions the VL may be above the limit of detection. Whether these 'blips' in VL are simply assay errors or are indicative of intermittent episodes of increased viral replication is of great clinical concern. By analyzing the occurrence of viral blips in 123 treated HIV-infected patients, we show that patients do not share a common probability distribution of blip amplitude and thus reject the hypothesis that blips are solely due to assay variation.

Antiretroviral Therapy, Highly Active↗

PubMed2002

Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand-receptor interactions: theory and application to HIV treatment.

In HIV-infected patients, large quantities of HIV are associated with follicular dendritic cells (FDCs) in lymphoid tissue. During antiretroviral therapy, most of this virus disappears after six months of treatment, suggesting that FDC-associated virus has little influence on the eventual outcome of long-term therapy. However, a recent theoretical study using a stochastic model for the interaction of HIV with FDCs indicated that some virus may be retained on FDCs for years, where it can potentially reignite infection if treatment is interrupted. In that study, an approximate expression was used to estimate the time an individual virion remains on FDCs during therapy. Here, we determine the conditions under which this approximation is valid, and we develop expressions for the time a virion spends in any bound state and for the effect of rebinding on retention. We find that rebinding, which is influenced by diffusion, may play a major role in retention of HIV on FDCs. We also consider the possibility that HIV is retained on B cells during therapy, which like FDCs also interact with HIV. We find that virus associated with B cells is unlikely to persist during therapy.

Anti-HIV Agents↗