arXiv subjects

M. W. C. Dharma-wardana

Publications and source records attributed to M. W. C. Dharma-wardana.

At least 19 recordsLinked to original sources

arXiv2025

A study of the electronic and ionic structure, for competing states of fully and partially ionized hydrogen, using the neutral pseudo-atom method as well as a classical map for the electron subsystem

Prof. Bonitz and his collaborators have made seminal contributions to the study of the uniform electron fluid and the electron-proton fluid, viz., hydrogen, in using {\it ab initio} simulations, as reflected in this festschrift. Here we review the theoretical methods available for these systems where traditional small-parameter methods fail. We use the neutral-pseudo atom (NPA) method, and a classical map for quantum electrons to study hydrogen plasmas. We show that {\it both} fully-ionized and partially-ionized hydrogen phases can exist with the same nominal density and temperature, at pressures and temperatures of interest to planetary physics. The mean ionization $\bar{Z}$, pair-distribution functions, free energies, pressures and conductivities are calculated for the competing phases. Here $\bar{Z}$ is also a measure of the miscibility of fully ionized and un-ionized hydrogen. Recent studies using path-integral Monte Carlo methods, and $N$-atom Density Functional Theory (DFT) simulations have provided essential structure data including the electron-electron structure factor $S_{ee}(k)$ that enters into interpretation of X-ray Thomson scattering and other diagnostics. We show that these structure data can be inexpensively evaluated using classical-map schemes for fully ionized plasmas, and more generally, using one-atom (average-atom) DFT methods for partially ionized systems.

physics.plasm-ph↗

arXiv2025

X-ray Thomson scattering studies on spin-singlet stabilization of highly compressed H-like Be ions heated to two million degrees Kelvin

Experiments at the US National Ignition Facility (NIF) [Döppner et al., Nature {\bf 618}, 270-275 (2023)] have created highly compressed hot hydrogen-like Be plasmas. Published analyses of the the NIF experiment have used finite-$T$ multi-atom density-functional theory (DFT) with Molecular dynamics (MD), and Path-Integral Monte Carlo (PIMC) simulations. These methods are very expensive to implement and often lack physical transparency. Here we (i) relate their results to simpler first-principles average-atom results, (ii) establish the feasibility of rapid data analysis, with good accuracy and gain in physical transparency, and (iii) show that the NIF experiment reveals high-$T$ spin-singlet pairing of hydrogen-like Be ions with near neighbours. Our analysis predicts such stabilization over a wide range of compressed densities for temperatures close to two million Kelvin. Calculations of structure factors $S(k)$ for electrons or ions, the Raleigh weight and other quantities of interest to X-ray Thomson scattering are presented. We find that the NIF data at the scattering wavevector $k_{sc}$ of 7.89 Å$^{-1}$ are more consistent with a density of $20\pm2$ g/cm$^3$, mean ionization $\bar{Z}=$3.25, at a temperature of $\simeq$ 1,800,000 K than the 34 g/cm$^3, \bar{Z}=3.4$ proposed by the NIF team. The relevance of ion-electron coupled-modes in studying small $k_{sc}$ data is indicated.

cond-mat.mtrl-sci↗

arXiv2024

Ionic structure, Liquid-liquid phase transitions, X-Ray diffraction, and X-Ray Thomson scattering in shock compressed liquid Silicon in the 100-200 GPa regime

Recent cutting-edge experiments have provided {\it in situ} structure characterization and measurements of the pressure ($P$), density ($\barρ$) and temperature ($T$) of shock compressed silicon in the 100 GPa range of pressures and upto $\sim$10,000K. We present first-principles calculations in this $P,T,\barρ$ regime to reveal a plethora of novel liquid-liquid phase transitions (LPTs) identifiable via discontinuities in the pressure and the compressibility. Evidence for the presence of a highly-correlated liquid (CL) phase, as well as a normal-liquid (NL) phase at the LPTs is presented by a detailed study of one LPT. The LPTs make the interpretation of these experiments more challenging. The LPTs preserve the short-ranged ionic structure of the fluid by collective adjustments of many distant atoms when subject to compression and heating, with minimal change in the ion-ion pair-distribution functions, and in transport properties such as the electrical and thermal conductivities $σ$ and $κ$. We match the experimental X-Ray Thomson scattering and X-ray diffraction data theoretically, and provide pressure isotherms, ionization data and compressibilities that support the above picture of liquid silicon as a highly complex LPT-driven ``glassy'' metallic liquid. These novel results are relevant to materials research, studies of planetary interiors, high-energy-density physics, and in laser-fusion studies.

cond-mat.mtrl-sci↗

arXiv2024

The finite-$T$ Lorentz number and the thermal conductivity. Aluminum and carbon conductivities from ambient to millions of degrees Kelvin

Theoretical prediction of the thermal conductivity $κ$ of metal-like electron-ion systems would be greatly simplified if a convenient generalization of the Lorentz number $L_N$ for arbitrary temperatures ($T$) and densities were available. Such calculations are needed in astrophysics, high-energy-density physics, semiconductor physics as well as in materials science. We present a finite-$T$ form of $L_N(T)$, expressed in terms of elementary Fermi integrals. It is a universal function of $t=T/E_F$, where $E_F$ is the Fermi energy of the electrons. A convenient four-parameter fit to $L_N(t)$ for $t=0-\infty$ further simplifies the applications. The effect of electron-electron interactions is also briefly discussed. Calculations for $L_N(t)$ and thermal conductivities $κ$ for Al and C are presented at several compressions and into the million-Kelvin range. Experimental isobaric conductivities for Al just above the meting point, and isochoric conductivities for Al and C from available density-functional theory simulations and average-atom calculations are used as comparisons.

cond-mat.mtrl-sci↗

arXiv2023

A critical examination of crop-yield data for vegetables, maize and Tea for commercialized Sri Lankan biofilm biofertilizers

With increasing global interest in microbial methods for agriculture, the commercialization of biofertilizers in Sri Lanka is of general interest. The use of a biofilm-biofertilizer (BFBF) commercialized in Sri Lanka is claimed to reduce chemical fertilizer (CF) usage by ~50 per cent while boosting harvest by 20-30 per cent. Many countries have explored the potential of biofilm biofertilizers, but have so far found mixed results. Here we review this BFBF commercialized in Sri Lanka and approved for nation-wide use there. We show in detail that the improved yields claimed for this BFBF fall within the uncertainties (error bars) of the harvest. Theoretical models that produce a seemingly reduced CF scenario with an "increase" in harvests, although this is in fact not so, are presented. While BFBF usage seems to improve soil quality in certain respects, the currently available BFBF promoted in Sri Lanka has negligible impact on crop yields. We also briefly consider the potential negative effects of large-scale adoption of microbial methods.

q-bio.OT↗

arXiv2022

Yukawa Friedel-Tail pair potentials for warm dense matter applications

Accurate equations of state (EOS) and plasma transport properties are essential for numerical simulations of warm dense matter encountered in many high-energy-density situations. Molecular dynamics (MD) is a simulation method that generates EOS and transport data using an externally provided potential to dynamically evolve the particles without further reference to the electrons. To minimize computational cost, pair potentials needed in MD may be obtained from the neutral-pseudoatom (NPA) approach, a form of single-ion density functional theory (DFT), where many-ion effects are included via ion-ion correlation functionals. Standard $N$-ion DFT-MD provides pair potentials via the force matching technique but at much greater computational cost. Here we propose a simple analytic model for pair potentials with physically meaningful parameters based on a Yukawa form with a thermally damped Friedel tail (YFT) applicable to systems containing free electrons. The YFT model accurately fits NPA pair potentials or the non-parametric force-matched potentials from $N$-ion DFT-MD, showing excellent agreement for a wide range of conditions. The YFT form provides accurate extrapolations of the NPA or force-matched potentials for small and large particle separations within a physical model. Our method can be adopted to treat plasma mixtures, allowing for large-scale simulations of multi-species warm dense matter.

cond-mat.stat-mech↗

arXiv2022

Evidence for multiple Liquid-liquid phase transitions in carbon, and the Friedel-ordering of its liquid state

Carbon, the fourth most abundant element in the Universe forms a metallic fluid with transient covalent bonds on melting. Its liquid-liquid phase transitions, intensely sought using simulations had been elusive. Here we use density functional theory (DFT) simulations with up to 108 atoms using molecular dynamics, as well as one-atom DFT as implemented in the neutral pseudo-atom method where multi-atom effects are treated by ion-ion correlation functionals. Both methods use electron-electron exchange correlation functionals for electron many-body effects. Here we show using both methods, that liquid carbon displays multiple liquid-liquid transitions linked to changes in coordination number in the density range 3 g/cm$^3$, to $\sim$ 6 g/cm$^3$ when a coordination number of 12 is reached. The transitions disappear by 4 eV in temperature. The calculated pressures and transition densities are shown to be sensitive to the exchange-correlation functionals used. Significantly, we find that a simple metallic model yields the structure factors and thermodynamics with quantitative accuracy, without invoking any covalent-bonding features. The ion-ion structure factor for these densities and temperatures is found to have a subpeak tied to twice the Fermi wavevector, constraining the fluid in momentum space. The dominant Friedel oscillations forming the pair interactions correlate the ions and drive the multiple liquid-liquid phase transitions. Our results suggest that liquid carbon typifies a class of fluids whose structure is ordered by the long-range Friedel oscillations in the pair-potentials. These results are critical to terrestrial and astrophysical studies, inertial fusion using carbon drivers, refined shock experiments, and in seeking new carbon-based materials.

cond-mat.stat-mech↗

arXiv2022

Comment on "Water sources and kidney function: investigating chronic kidney disease of unknown etiology in a prospective study", by P. Vlahos et al

Vlahos et al., Ref. 1, NPJ Clean water. 4, 50 (2021) have reported the presence of pesticide contamination above safe levels in a "single time-point analysis" of well water in a region in Sri Lanka where chronic kidney disease of unknown etiology (CKDu) is endemic. They conclude "that agrochemical use in paddy and other agricultural practices ... of the Green Revolution in Sri Lanka may now be contributing to ill health, rapid progression of disease, and mortality". The authors also propose "reducing ... agrochemical contaminants in Sri Lanka and other tropical countries to reduce ... CKDu". These conclusions, based on what they call a "single time-point analysis", tantamount to an identification of the etiology of CKDu are unsupported by the evidence presented by Vlahos et al. They do not satisfy, say, even the simplest of Bradford-Hill criteria for causation. In particular, (i) similar but non-persistent pesticide excesses have been detected sporadically in most parts of the country including where there is no CKDu; (ii) the pesticides reported in (1) cause both hepatotoxicity and nephrotoxicity; the latter with glomerular damage while CKDu is associated with tubulo-interstitial damage where no hepatotoxic symptoms have been reported; (iii) the pesticides detected have short half-lives and are used over short periods during farming; so the one time-point analysis is inadequate and misleading; (iv) farming communities that use pesticides in the same way but remain essentially without CKDu are found to exist adjacent to communities with CKDu; (v) the CKDu prevalence seems to correlate with local geomorphology but without correlation to agriculture which is practiced in most parts of the country. .

q-bio.TO↗

arXiv2021

The ionization of carbon at 10-100 times the diamond density and in the 10$^6$ K temperature range

The behaviour of partially ionized hot compressed matter is critical to the study of planetary interiors as well as for nuclear fusion studies. A recent quantum study of carbon in the 10-70 Gbar range and at a temperature of 100 eV used $N$-atom density functional theory (DFT) with $N\sim 32$-64 and molecular dynamics (MD). This involves band-structure type electronic calculations and averaging over many MD generated ion configurations. The calculated average number of free electrons per ion, viz., $\bar{Z}$, was systematically higher than from a standard average atom (AA) quantum calculation. To clarify this offset, we examine (a) the effect of the self-interaction (SI) error in such estimates (b) the possibility of carbon being a granular plasma containing Coulomb crystals. The possibility of `magic-number' bound states is considered. The electrical conductivity, pressure, and the compressibility of the carbon system are examined. The very low conductivity and the high $\bar{Z}$ results of DFT-MD point to the existence of carbon in a complex non-uniform low-conducting dispersed phase, possibly containing magic-number Coulomb crystals. The NPA estimate of $\bar{Z}$, conductivity, compressibility, and pressure reported here pertain to the {\it uniform liquid}.

physics.plasm-ph↗

arXiv2021

Simple pair-potentials and pseudo-potentials for warm-dense matter and general applications

We present methods for generating computationally simple parameter-free pair potentials useful for solids, liquids and plasma at arbitrary temperatures. They successfully treat warm-dense matter (WDM) systems like carbon or silicon with complex tetrahedral or other structural bonding features. Density functional theory asserts that only one-body electron densities, and one-body ion densities are needed for a complete description of electron-ion systems. DFT is used here to reduce {\it both} the electron many-body problem and the ion many-body problem to an exact one-body problem, namely that of the neutral pseudoatom (NPA). We compare the Stillinger-Weber (SW) class of multi-center potentials, and the embedded-atom approaches, with the NPA approach to show that many-ion effects are systematically included in this one-center method via one-body exchange-correlation functionals. This computationally highly efficient "single-center" DFT-NPA approach is contrasted with the usual $N$-center DFT calculations that are coupled with molecular dynamics (MD) simulations to equilibriate the ion distribution. Comparisons are given with the pair-potential parts of the SW, effective-medium `glue' models, and the corresponding NPA pair-potentials to elucidate how the NPA potentials capture many-center effects using only pair-potentials, based on single-center one-body densities.

cond-mat.mtrl-sci↗

arXiv2020

Efficacy of the Radial Pair Potential Approximation for Molecular Dynamics Simulations of Dense Plasmas

Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale simulation methods by comparing Kohn-Sham density functional theory molecular dynamics (KS-MD) and radial pair potential molecular dynamics (RPP- MD) for a range of elements, temperature, and density. By extracting the optimal RPP from KS-MD data using force-matching, we constrain its functional form and dismiss classes of potentials that assume a constant power law for small interparticle distances. Our results show excellent agreement between RPP-MD and KS-MD for multiple metrics of accuracy at temperatures of only a few electron volts. The use of RPPs offers orders of magnitude decrease in computational cost and indicates that three-body potentials are not required beyond temperatures of a few eV. Due to its efficiency, the validated RPP-MD provides an avenue for reducing errors due to finite-size effects that can be on the order of $\sim20\%$.

physics.plasm-ph↗

arXiv2020

Review of the First Charged-Particle Transport Coefficient Comparison Workshop

We present the results of the first Charged-Particle Transport Coefficient Code Comparison Workshop, which was held in Albuquerque, NM October 4-6, 2016. In this first workshop, scientists from eight institutions and four countries gathered to compare calculations of transport coefficients including thermal and electrical conduction, electron-ion coupling, inter-ion diffusion, ion viscosity, and charged particle stopping powers. Here, we give general background on Coulomb coupling and computational expense, review where some transport coefficients appear in hydrodynamic equations, and present the submitted data. Large variations are found when either the relevant Coulomb coupling parameter is large or computational expense causes difficulties. Understanding the general accuracy and uncertainty associated with such transport coefficients is important for quantifying errors in hydrodynamic simulations of inertial confinement fusion and high-energy density experiments.

physics.plasm-ph↗

arXiv2020

Liquid-liquid Phase transitions in silicon

We use computationally simple neutral pseudo-atom (`average atom') one-center density functional theory (DFT) and standard N-center DFT-Molecular Dynamics simulations to elucidate liquid-liquid phase transitions (LPTs) in supercooled liquid silicon at 1200K ,and also in silicon under warm-dense matter conditions up to 11604k (1 eV). An ionization-driven transition and three LPTs including the known LPT near 2.5 g/cm$^3$ are found. They are robust even to 1 eV. The pair distributions functions, pair potentials, electrical conductivities, and compressibilites are reported. The LPTs are elucidated within a Fermi liquid picture of electron scattering at the Fermi energy that complements the usual transient covalent bonding picture.

cond-mat.mtrl-sci↗

arXiv2020

Discussion on a "Dynamic model to conceptualize multiple environmental pathways to the epidemic of Chronic Kidney Disease of unknown etiology (CKDu)"

Jayasinghe et al. [Science of the Total Environment, 705 (2020) 135766] propose a 'dynamical' model of Chronic Kidney Disease of Unknown etiology (CKDu) wherein CKDu arises as an emergent property of a complex system where they claim that weak multiple environmental factors contribute. They criticize the usual approaches as being "reductionist". We use their model as a basis of a discussion on the possibility of treating CKDu as an emergent property resulting from the interaction of multiple weak environmental factors with the organism. The model does not reveal anything beyond what is already known from simple considerations of well-known feed-back loops, but has the merit of re-stating those issues in a different format. If a proper weighting of the possible environmental factors is included, most proposed environmental factors drop out and what Jayasinghe et al. call the "reductionist" approach naturally arises due to the weight of evidence. The theory that the consumption of water containing fluoride and magnesium ions as found in water from regolith aquifers drawn via house-hold wells is found to clearly hold within this model when proper weighting is included. However, we show by examples that such models can be easily misused, leading to completely misleading conclusions. A response formalism useful in the theory of complex systems and emergent modes is presented in the context of the current problem. In addition to there being a lack of adequate data to fully implement such a theory, it is seen that such elaborations are unnecessary and misleading in the present context.

q-bio.QM↗

arXiv2019

Kinetic energy functionals and the $N$-representability of the electron pair-density given by the classical map hyper-netted-chain (CHNC) method

The classical map hypernetted-chain (CHNC) method for interacting electrons uses a kinetic energy functional in the form of a classical-fluid temperature. Here we show that the CHNC generated two-body densities and pair-distribution functions (PDFs) correspond to $N$-representable densities. Comparisons of results from CHNC with quantum Monte Carlo (QMC) and Path Integral Monte Carlo (PIMC) are used to validate the CHNC results. Since the PDFs are sufficient to obtain the equation of state or linear-response properties of electron-ion systems, we apply the CHNC method for fully classical calculations of electron-ion systems in the quantum regime, using hydrogen at 4000K and 350 times the solid density as an example since QMC comparisons are available. We also present neutral pseudo-atom (NPA) calculations which use rigorous density-functional theory (DFT) to reduces the many nuclear problem to an effective one-ion problem. The CHNC PDFs and NPA results agree well with the ion-ion, electron-ion and electron-electron PDFs from QMC, PIMC, or DFT coupled to molecular dynamics simulations where available. The PDFs of a 2D electron-hole system at 5K are given as an example of 2D `warm dense' matter where the electrons and the counter particles (holes) are all in the quantum regime. Basic methods like QMC, PIMC or even DFT become prohibitive while CHNC methods, being independent of the number of particles or the temperature, prove to be easily deployable.

cond-mat.stat-mech↗

arXiv2019

Reply to comment by Witte et al. on "Isochoric, isobaric, and ultrafast conductivities of aluminum, lithium,and carbon in the warm dense matter regime", Phys. Rev. E $96$, 053206 (2017)

In Phys. Rev. E, $99$, 047201 (2019) Witte {\it et al.} have commented on our conductivity calculations [Phys. Rev. E $96$, 053206 (2017)] for warm dense matter (WDM). (i) They criticize our use of the spherically-averaged structure factor $S(k)$ for calculations of the static conductivity $σ$ of FCC aluminum - a common approximation for polycrystalline materials. They themselves give no calculations as their method using density-functional theory (DFT) and molecular dynamics (MD) based Kubo-Greenwood (KG) calculations becomes impractical for cold ions. (ii) We are satisfied that Witte et al. no longer claim a factor of $\sim$ 1.5 change in $σ$ on changing the exchange-correlation (XC) functional used. (iii) They have provided computer-intensive calculations of $σ$ for aluminum using DFT-MD-KG simulations, for temperatures $T$ up to 15 eV but using only $N$=64 atoms in the simulation, where as a mixture of ionic species needs a far larger $N$ to be credible. We present multi-species conductivity calculations via a parameter-free DFT theory [Phys. Rev. E. $52$, 5352 (1995)] for 5 eV to 50 eV. (iv) The conductivities obtained from well-converged DFT-MD-KG methods show a significant underestimate of $σ$; this is especially evident for the isochoric conductivity $σ_{\rm ic}$ extrapolating to $\sim3.5\times 10^6$ S/m, i.e, {\it even below} the experimental {\it isobaric} value of 4.1$\times 10^6$ S/m at the melting point, when a value of $\sim 5\times 10^6$ S/m is anticipated.

cond-mat.stat-mech↗

arXiv2019

Correlation functions in electron-electron and electron-hole double quantum wells: Temperature, density and barrier-width dependence

The classical-map hyper-netted-chain (CHNC) scheme, developed for treating fermion fluids at strong coupling and at finite temperatures, is applied to electron-electron and electron-hole double quantum wells. The pair distribution functions and the local field factors needed in linear response theory are determined for a range of temperatures, carrier densities, and barrier widths typical for experimental double quantum well systems in GaAs-GaAlAs. For electron-hole double quantum wells, a large enhancement in the pair distribution functions is found for small carrier separations. The CHNC equations for electron-hole systems no longer hold at low densities where bound-state formation occurs.

cond-mat.mes-hall↗

arXiv2018

Fertilizer usage and cadmium in soils, crops and food

Phosphate fertilizers were first implicated by Schroeder and Balassa in 1963 for increasing the Cd concentration in cultivated soils and crops. This suggestion has become a part of the accepted paradigm on soil toxicity. Consequently, stringent fertilizer control programs to monitor Cd have been launched. Attempts to link Cd toxicity and fertilizers to chronic diseases are common. A re-assessment of this "accepted" paradigm is timely, given the larger body of data available today. The data show that both the input and output of Cd per hectare from fertilizers are negligibly small compared to the total amount of Cd/hectare usually present in the soil itself. Calculations based on current agricultural practices are used to show that it will take about 18 centuries to double the ambient soil-cadmium level, and about 8 centuries to double the soil-fluoride level, even after neglecting leaching and other removal effects. Hence the concern of long-term agriculture should be the depletion of available phosphate fertilizers, rather than the contamination of the soil by trace metals or fluoride. This conclusion is confirmed by showing that the claimed correlations between fertilizer input and cadmium accumulation in crops are not robust. Alternative scenarios that explain the data are examined. Thus soil acidulation on fertilizer loading, and the effect of magnesium, zinc, and fluoride ions contained in fertilizers are considered using recent Cd$^{2+}$, Mg$^{2+}$ and F$^-$ ion-association theories. The protective role of ions like Zn, Se, Fe, etc., is emphasized, and the question of cadmium toxicity in the presence of other ions is considered. These help to clarify and rectify difficulties found in the standard point of view. This analysis does not modify the accepted views on Cd contamination by airborne delivery, smoking, and industrial activity, or P-contamination causing algal blooms.

q-bio.TO↗