المؤلفون: Jing, Xin, Suryanarayana, Phanish

مصطلحات موضوعية: Physics - Computational Physics, Condensed Matter - Materials Science, Physics - Chemical Physics

الوصف: We present an efficient real space formalism for hybrid exchange-correlation functionals in generalized Kohn-Sham density functional theory (DFT). In particular, we develop an efficient representation for any function of the real space finite-difference Laplacian matrix by leveraging its Kronecker product structure, thereby enabling the time to solution of associated linear systems to be highly competitive with the fast Fourier transform scheme, while not imposing any restrictions on the boundary conditions. We implement this formalism for both the unscreened and range-separated variants of hybrid functionals. We verify its accuracy and efficiency through comparisons with established planewave codes for isolated as well as bulk systems. In particular, we demonstrate up to an order-of-magnitude speedup in time to solution for the real space method. We also apply the framework to study the structure of liquid water using ab initio molecular dynamics, where we find good agreement with literature. Overall, the current formalism provides an avenue for efficient real space DFT calculations with hybrid density functionals.
Comment: 9 pages, 4 figures

الوصول الحر: http://arxiv.org/abs/2406.16998Test

المؤلفون: Bhowmik, Sayan, Pask, John E., Medford, Andrew J., Suryanarayana, Phanish

مصطلحات موضوعية: Physics - Computational Physics, Condensed Matter - Materials Science

الوصف: We present a spectral scheme for atomic structure calculations in pseudopotential Kohn-Sham density functional theory. In particular, after applying an exponential transformation of the radial coordinates, we employ global polynomial interpolation on a Chebyshev grid, with derivative operators approximated using the Chebyshev differentiation matrix, and integrations using Clenshaw-Curtis quadrature. We demonstrate the accuracy and efficiency of the scheme through spin-polarized and unpolarized calculations for representative atoms, while considering local, semilocal, and hybrid exchange-correlation functionals. In particular, we find that $\mathcal{O}$(200) grid points are sufficient to achieve an accuracy of 1 microhartree in the eigenvalues for optimized norm conserving Vanderbilt pseudopotentials spanning the periodic table from atomic number $Z = 1$ to $83$.
Comment: 21 pages, 7 figures, 4 tables

الوصول الحر: http://arxiv.org/abs/2406.00534Test

المؤلفون: Gupta, Nishant, Suryanarayana, Nemani V.

مصطلحات موضوعية: High Energy Physics - Theory, General Relativity and Quantum Cosmology

الوصف: We propose mixed boundary conditions for 3d conformal gravity consistent with variational principle in its second-order formalism that admit the chiral $\Lambda$-$\mathfrak{bms}_4$ algebra as their asymptotic symmetry algebra. This algebra is one of the four chiral $\mathcal W$-algebra extensions of $\mathfrak{so}(2,3)$ and is a generalisation of the chiral $\mathfrak{bms}_4$ algebra responsible for soft theorems of graviton MHV amplitudes in ${\mathbb R}^{1,3}$ gravity to the case of non-zero negative cosmological constant. The corresponding charges calculated using the modified covariant phase space formalism are shown to be finite and integrable, and realise this non-linear ${\cal W}$-algebra.
Comment: 22 pages

الوصول الحر: http://arxiv.org/abs/2405.20244Test

المؤلفون: Timmerman, Lucas R., Kumar, Shashikant, Suryanarayana, Phanish, Medford, Andrew J.

مصطلحات موضوعية: Physics - Computational Physics, Condensed Matter - Materials Science, Physics - Chemical Physics

الوصف: We develop a framework for on-the-fly machine learned force field molecular dynamics simulations based on the multipole featurization scheme that overcomes the bottleneck with the number of chemical elements. Considering bulk systems with up to 6 elements, we demonstrate that the number of density functional theory calls remains approximately independent of the number of chemical elements, in contrast to the increase in the smooth overlap of atomic positions scheme.
Comment: 15 total pages including references and SI, 4 main figures, 1 supplemental, 6 supplemental tables. Submitted to ACS Journal of Chemical Theory and Computation. Written and reviewed by all

الوصول الحر: http://arxiv.org/abs/2404.07961Test

المؤلفون: Kumar, Shashikant, Jing, Xin, Pask, John E., Suryanarayana, Phanish

مصطلحات موضوعية: Physics - Computational Physics, High Energy Physics - Theory

الوصف: We develop a framework for on-the-fly machine learned force field (MLFF) molecular dynamics (MD) simulations of warm dense matter (WDM). In particular, we employ an MLFF scheme based on the kernel method and Bayesian linear regression, with the training data generated from Kohn-Sham density functional theory (DFT) using the Gauss Spectral Quadrature method, within which we calculate energies, atomic forces, and stresses. We verify the accuracy of the formalism by comparing the predicted properties of warm dense carbon with recent Kohn-Sham DFT results in the literature. In so doing, we demonstrate that ab initio MD simulations of WDM can be accelerated by up to three orders of magnitude, while retaining ab initio accuracy. We apply this framework to calculate the diffusion coefficients and shear viscosity of CH at a density of 1 g/cm$^3$ and temperatures in the range of 75,000 to 750,000 K. We find that the self- and inter-diffusion coefficients as well as the viscosity obey a power law with temperature, and that the diffusion coefficient results suggest a weak coupling between C and H in CH. In addition, we find agreement within standard deviation with previous results for C and CH but disagreement for H, demonstrating the need for ab initio calculations as presented here.
Comment: 9 pages, 5 figures, 2 tables

الوصول الحر: http://arxiv.org/abs/2402.13450Test

المؤلفون: Ashktorab, Hassan, Challa, Suryanarayana, Singh, Gagan, Nanduri, Sumant, Ibrahim, Malika, Martirosyan, Zara, Whitsell, Peter, Chirumamilla, Lakshmi, Shayegh, Nader, Watson, Kyra, Smith, Tori, Ogwo, Valarie, Kolawole, Oluwapelumi, Littleton, Megan, Morrison, Nicole, Nair, Vaisakh, Byer, Danae, Dawodu, Dideolu, Lexima, Patrice, Rashid, Mudasir, Deverapalli, Mrinalini, Atluri, Swetha, Nezamloo, Ali, Nasrin, Farjana, Kim, Rachel, Sherif, Zaki, Oskrochi, Gholamreza, Brim, H, Carethers, John

المصدر: Digestive Diseases and Sciences. 69(2)

مصطلحات موضوعية: African Americans, And Mini-MoCA, Gastrointestinal manifestations, Long-COVID, PASC, Sleep problems, Female, Humans, Male, COVID-19, SARS-CoV-2, Follow-Up Studies, Post-Acute COVID-19 Syndrome, Prospective Studies, COVID-19 Vaccines, Gastrointestinal Diseases, Liver Diseases, Vomiting, Sleep Wake Disorders

الوصف: BACKGROUND: Long-COVID is a condition post SARS-CoV-2 infection with persistent or recurring symptoms affecting multiple organs, and may involve viral persistence, changes to the microbiome, coagulopathies, and alterations to neuro-immune interactions. These factors can disrupt the Gut-Brain Axis, which is a complex system involving bidirectional communication between the central nervous system and the gastrointestinal (GI) system. As a result of these disruptions, individuals with long-COVID may develop post-infectious functional GI disorders, which can cause a range of symptoms affecting the digestive system. AIM: To understand frequency of GI manifestations of Long-COVID and to determine association with sleep or neurological symptoms in a predominantly minority population. METHODS: We included patients with positive SARS-CoV-2 PCR (n = 747) who were hospitalized from Feb. 2020 to May 2021 at Howard University Hospital and followed between 6 and 12 months from discharge. GI, sleep, and neurological symptoms (via the Montreal Cognitive Assessment (MoCA) scoring system) were assessed using a standardized questionnaire. Linear regression analysis, χ2 and Fishers exact test were utilized to determine the statistical significance of correlations of GI/Neuro/COVID. RESULTS: The mean age of patients was 58, with 51.6% females and a predominant African American ethnicity (73.6%, n = 550). A total of 108 patients died during their initial hospital stay, with the remaining 639 patients followed-up. Three hundred fifty (350) patients responded to the questionnaire (57 patients died during the follow-up period). Overall, 39 (13.3%) patients reported GI-related symptoms, out of which 19 (6.4%) had persistent symptoms and 20 (6.8%) developed new onset GI symptoms. Nausea and vomiting were the most common 24/39 (61.5%), followed by abdominal pain 7/39 (18%), diarrhea 5/39 (12.8%), and others 3/39 (7.6%). Patients who presented with vomiting during acute SARS-CoV-2 infection were more likely to have Long-COVID GI manifestations (P = 0.023). Use of ACE inhibitors, abnormal lymphocyte count and elevated ferritin are other variables that showed significant associations with Long-COVID GI manifestations (P = 0.03, 0.006 and 0.03, respectively). During follow-up, a total of 28 (9.5%) patients reported difficulty with sleep and 79 (27%) patients had abnormal MoCA assessment. With further analysis, there was a trend between presentation of GI symptoms on admission with abnormal MoCA assessment, and an association between abnormal LFTs and history of liver disease during hospitalization with subsequent sleep problems. Baseline characteristics, clinical comorbidities, other laboratory values, hospital length of stay, mechanical ventilation, medications during hospitalization, re-admission and Flu or COVID-19 vaccination have not shown any association with Long-COVID GI symptoms in our cohort. CONCLUSION: Dyspeptic symptoms were common GI manifestations in the acute and post COVID periods. GI symptoms, abnormal LFTs and a history of liver disease during the acute infectious phase associates with abnormal MoCA and sleep problems during follow-up. Further large population studies are needed to determine if COVID-19 leads to a GI symptoms-associated Long-COVID phenotypes and other symptoms through the Gut-Brain-Axis.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7b8572k4Test

المؤلفون: Biswas, Rahul, Sripada, SuryaNarayana, Mukherjee, Somabha

مصطلحات موضوعية: Statistics - Methodology, Quantitative Biology - Neurons and Cognition, Quantitative Biology - Quantitative Methods, Statistics - Applications

الوصف: Inferring causation from time series data is of scientific interest in different disciplines, particularly in neural connectomics. While different approaches exist in the literature with parametric modeling assumptions, we focus on a non-parametric model for time series satisfying a Markovian structural causal model with stationary distribution and without concurrent effects. We show that the model structure can be used to its advantage to obtain an elegant algorithm for causal inference from time series based on conditional dependence tests, coined Causal Inference in Time Series (CITS) algorithm. We describe Pearson's partial correlation and Hilbert-Schmidt criterion as candidates for such conditional dependence tests that can be used in CITS for the Gaussian and non-Gaussian settings, respectively. We prove the mathematical guarantee of the CITS algorithm in recovering the true causal graph, under standard mixing conditions on the underlying time series. We also conduct a comparative evaluation of performance of CITS with other existing methodologies in simulated datasets. We then describe the utlity of the methodology in neural connectomics -- in inferring causal functional connectivity from time series of neural activity, and demonstrate its application to a real neurobiological dataset of electro-physiological recordings from the mouse visual cortex recorded by Neuropixel probes.

الوصول الحر: http://arxiv.org/abs/2312.09604Test

المؤلفون: Chaudhuri, Kalyani, Jha, Natasha, Nilayamgode, Mrithyunjayan, Suryanarayana, Revathy

مصطلحات موضوعية: Development Studies, Economics, Applied Economics, Human Society, Applied economics, Development studies

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/6h79s0kxTest
https://escholarship.org/content/qt6h79s0kx/qt6h79s0kx.pdfTest

المؤلفون: Ashktorab, Hassan, Pizuorno, Antonio, Chirumamilla, Lakshmi, Adeleye, Folake, Dalivand, Maryam, Sherif, Zaki, Oskrochi, Gholamreza, Challa, Suryanarayana, Jones-Wonni, Boubini, Rankine, Sheldon, Ekwunazu, Chiamaka, Banson, Abigail, Kim, Rachel, Gilliard, Chandler, Ekpe, Elizabeth, Shayegh, Nader, Nyaunu, Constance, Martins, Chidi, Slack, Ashley, Okwesili, Princess, Abebe, Malachi, Batta, Yashvardhan, Ly, Do, Valarie, Ogwo, Smith, Tori, Watson, Kyra, Kolawole, Oluwapelumi, Tahmazian, Sarine, Atoba, Sofiat, Khushbakht, Myra, Riley, Gregory, Gavin, Warren, Kara, Areeba, Hache-Marliere, Manuel, Palaiodimos, Leonidas, Mani, Vishnu, Kalabin, Aleksandr, Gayam, Vijay, Garlapati, Pavani, Miller, Joseph, Jackson, Fatimah, Rustgi, Vinod, Brim, Hassan, Carethers, John

مصطلحات موضوعية: African Americans, COVID-19, Mortality, United States

الوصف: BACKGROUND AND AIM: Identifying clinical characteristics and outcomes of different ethnicities in the US may inform treatment for hospitalized COVID-19 patients. Aim of this study is to identify predictors of mortality among US races/ethnicities. DESIGN SETTING AND PARTICIPANTS: We retrospectively analyzed de-identified data from 9,873 COVID-19 patients who were hospitalized at 15 US hospital centers in 11 states (March 2020-November 2020). Main Outcomes and Measures: The primary outcome was to identify predictors of mortality in hospitalized COVID-19 patients. RESULTS: Among the 9,873 patients, there were 64.1% African Americans (AA), 19.8% Caucasians, 10.4% Hispanics, and 5.7% Asians, with 50.7% female. Males showed higher in-hospital mortality (20.9% vs. 15.3%, p=0.001). Non- survivors were significantly older (67 vs. 61 years) than survivors. Patients in New York had the highest in-hospital mortality (OR=3.54 (3.03 - 4.14)). AA patients possessed higher prevalence of comorbidities, had longer hospital stay, higher ICU admission rates, increased requirement for mechanical ventilation and higher in-hospital mortality compared to other races/ethnicities. Gastrointestinal symptoms (GI), particularly diarrhea, were more common among minority patients. Among GI symptoms and laboratory findings, abdominal pain (5.3%, p=0.03), elevated AST (n=2653, 50.2%, p=

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/8ck1h2tsTest

المؤلفون: Wu, Cairn, Mulakaluri, Ashley, Chaurasia, Pranay, Suryanarayana, Sindhu, Singh, Ambreen, Krauss, Nicole, Tahir, Peggy, Elder, Charles, Puthiyedath, Rammanohar, Dhruva, Anand

المصدر: Journal of Ayurveda and Integrative Medicine. 15(1)

مصطلحات موضوعية: Adaptogens, Ayurveda, Ayurvedic medicine, Botanical medicine, Cancer, Dietary supplements, Natural products, Oncology

الوصف: INTRODUCTION: Rasayanas are Ayurvedic natural products that have adaptogenic effects. The extensive research on rasayanas in oncology is not currently well summarized. The aim of this review is to investigate the range and nature of the current body of research, identify gaps in knowledge, and to summarize the existing literature as it relates to Ayurvedic rasayanas and oncology. MATERIALS AND METHODS: A comprehensive literature search of fifteen Ayurvedic adaptogen rasayanas was conducted using three main concepts: Ayurvedic herbal terms, neoplasm terms, and oncological pathways. After screening was performed, key variables were extracted (tagged) including type of adaptogen, cancer type, type of study design, constituent type, and mechanisms of action (MOA). The results were synthesized and summarized using descriptive statistics and narrative summaries. RESULTS: Five hundred and eighty-four articles were reviewed and tagged. The two most tagged adaptogens were Glycyrrhiza glabra (Yashthimadhu/licorice) (n = 166 (28.4 %)) and Withania somnifera (Ashwagandha) (n = 151 (25.9 %)). The most frequently tagged cancer diagnostic categories were gastrointestinal (n = 175 (30 %)), and breast (n = 126 (21 %)). Most of the articles focused on in vitro studies (n = 470 (80.3 %)). Of the 12 MOA tags, the most frequently tagged was apoptosis (n = 298 (29.2 %)). CONCLUSION: A large body of pre-clinical literature exists on adaptogen rasayanas in oncology, indicating this field of research is still in its early phase. Comparatively few studies focused on the effects on the immune system. Given the growing interest in immuno-oncology therapeutics and the potential impact of adaptogen rasayanas on the immune system, future research may focus more in this area, along with work that is more directly linked to future clinical studies.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/6xb9s19nTest