85 research outputs found
<i>Ab Initio</i> Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique
Here,
we demonstrate the application of fragment-based electronic
structure calculations in (a) <i>ab initio</i> molecular
dynamics (AIMD) and (b) reduced dimensional potential calculations,
for medium- and large-sized protonated water clusters. The specific
fragmentation algorithm used here is derived from ONIOM, but includes
multiple, overlapping “model” systems. The interaction
between the various overlapping model systems is (a) approximated
by invoking the principle of inclusion-exclusion at the chosen higher
level of theory and (b) within a real calculation performed at the
chosen lower level of theory. The fragmentation algorithm itself is
written using bit-manipulation arithmetic, which will prove to be
advantageous, since the number of fragments in such methods has the
propensity to grow exponentially with system size. Benchmark calculations
are performed for three different protonated water clusters: H<sub>9</sub>O<sub>4</sub><sup>+</sup>,
H<sub>13</sub>O<sub>6</sub><sup>+</sup> and HÂ(H<sub>2</sub>O)<sub>21</sub><sup>+</sup>. For potential energy surface benchmarks, we sample the normal
coordinates and compare our surface energies with full MP2 and CCSDÂ(T)
calculations. The mean absolute error for the fragment-based algorithm
is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07
kcal/mol, when compared with CCSDÂ(T) calculations over 693 different
geometries for the H<sub>9</sub>O<sub>4</sub><sup>+</sup> system. For the larger HÂ(H<sub>2</sub>O)<sub>21</sub><sup>+</sup> water cluster,
the mean absolute error is on the order of a 0.1 kcal/mol, when compared
with full MP2 calculations for 84 different geometries, at a fraction
of the computational cost. <i>Ab initio</i> dynamics calculations
were performed for H<sub>9</sub>O<sub>4</sub><sup>+</sup> and H<sub>13</sub>O<sub>6</sub><sup>+</sup>, and the energy conservation was found
to be of the order of 0.01 kcal/mol for short trajectories (on the
order of a picosecond). The trajectories were kept short because our
algorithm does not currently include dynamical fragmentation, which
will be considered in future publications. Nevertheless, the velocity
autocorrelation functions and their Fourier transforms computed from
the fragment-based AIMD approaches were found to be in excellent agreement
with those computed using the respective higher level of theory from
the chosen hybrid calculation
Direct Atomic-Scale Observation of Intermediate Pathways of Melting and Crystallization in Supported Bi Nanoparticles
Uncovering
the evolutional pathways of melting and crystallization
atomically is critical to understanding complex microscopic mechanism
of first-order phase transformation. We conduct in situ atomic-scale
observations of melting and crystallization in supported Bi nanoparticles
under heating and cooling within an aberration-corrected TEM. We provide
direct evidence of the multiple intermediate state events in melting
and crystallization. The melting of the supported nanocrystal involves
the formation and migration of domain boundaries and dislocations
due to the atomic rearrangement under heating, which occurs through
a size-dependent multiple intermediate state. A critical size, which
is key to inducing the transition pathway in melting from two to four
barriers, is identified for the nanocrystal. In contrast, crystallization
of a Bi droplet involves three stages. These findings demonstrate
that the phase transformations cannot be viewed as a simple single
barrier-crossing event but as a complex multiple intermediate state
phenomenon, highlighting the importance of nonlocal behaviors
Efficient, “On-the-Fly”, Born–Oppenheimer and Car–Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure
We recently developed two fragment
based <i>ab initio</i> molecular dynamics methods, and in
this publication we have demonstrated
both approaches by constructing efficient classical trajectories in
agreement with trajectories obtained from “on-the-fly”
CCSD. The dynamics trajectories are obtained using both Born–Oppenheimer
and extended Lagrangian (Car–Parrinello-style) options, and
hence, here, for the first time, we present Car–Parrinello-like
AIMD trajectories that are accurate to the CCSD level of post-Hartree–Fock
theory. The specific extended Lagrangian implementation used here
is a generalization to atom-centered density matrix propagation (ADMP)
that provides post-Hartree–Fock accuracy, and hence the new
method is abbreviated as ADMP-pHF; whereas the Born–Oppenheimer
version is called frag-BOMD. The fragmentation methodology is based
on a set-theoretic, inclusion-exclusion principle based generalization
of the well-known ONIOM method. Thus, the fragmentation scheme contains
multiple overlapping “model” systems, and overcounting
is compensated through the inclusion-exclusion principle. The energy
functional thus obtained is used to construct Born–Oppenheimer
forces (frag-BOMD) and is also embedded within an extended Lagrangian
(ADMP-pHF). The dynamics is tested by computing structural and vibrational
properties for protonated water clusters. The frag-BOMD trajectories
yield structural and vibrational properties in excellent agreement
with full CCSD-based “on-the-fly” BOMD trajectories,
at a small fraction of the cost. The asymptotic (large system) computational
scaling of both frag-BOMD and ADMP-pHF is inferred as O(N3.5), for on-the-fly CCSD accuracy. The extended
Lagrangian implementation, ADMP-pHF, also provides structural features
in excellent agreement with full “on-the-fly” CCSD calculations,
but the dynamical frequencies are slightly red-shifted. Furthermore,
we study the behavior of ADMP-pHF as a function of the electronic
inertia tensor and find a monotonic improvement in the red-shift as
we reduce the electronic inertia. In all cases a uniform spectral
scaling factor, that in our preliminary studies appears to be independent
of system and independent of level of theory (same scaling factor
for both MP2 and CCSD implementations ADMP-pHF and for ADMP DFT),
improves on agreement between ADMP-pHF and full CCSD calculations.
Hence, we believe both frag-BOMD and ADMP-pHF will find significant
utility in modeling complex systems. The computational power of frag-BOMD
and ADMP-pHF is demonstrated through preliminary studies on a much
larger protonated 21-water cluster, for which AIMD trajectories with
“on-the-fly” CCSD are not feasible
Endosomal-Escape Polymers Based on Multicomponent Reaction-Synthesized Monomers Integrating Alkyl and Imidazolyl Moieties for Efficient Gene Delivery
As
one of the toughest tasks in the course of intracellular therapeutics
delivery, endosomal escape must be effectively achieved, particularly
for intracellular gene transport. In this report, novel endosomal-escape
polymers were designed and synthesized from monomers by integrating
alkyl and imidazolyl via Passerini reaction and reversible addition–fragmentation
chain transfer polymerization (RAFT). After introducing the endosomal-escape
polymers with proper degrees of polymerization (DPs) into polyÂ(2-dimethylaminoethyl
methacrylate) (PDMAEMA) as the gene delivery vectors, the block copolymers
exhibited significantly enhanced hemolytic activity at endosomal pH,
and the plasmid DNA (pDNA)-loaded polyplexes showed efficient endosomal
escape compared with PDMAEMA, ultimately achieving dramatically increased
gene transfection efficacy. These results suggest that the polymers
that integrate alkyl and imidazolyl moieties for efficient endosomal
escape have wide potential applications for intracellular gene delivery
<i>In Situ</i> Atomic-Scale Observation of Droplet Coalescence Driven Nucleation and Growth at Liquid/Solid Interfaces
Unraveling
dynamical processes of liquid droplets at liquid/solid
interfaces and the interfacial ordering is critical to understanding
solidification, liquid-phase epitaxial growth, wetting, liquid-phase
joining, crystal growth, and lubrication processes, all of which are
linked to different important applications in material science. In
this work, we observe direct <i>in situ</i> atomic-scale
behavior of Bi droplets segregated on SrBi<sub>2</sub>Ta<sub>2</sub>O<sub>9</sub> by using aberration-corrected transmission electron
microscopy and demonstrate ordered interface and surface structures
for the droplets on the oxide at the atomic scale and unravel a nucleation
mechanism involving droplet coalescence at the liquid/solid interface.
We identify a critical diameter of the formed nanocrystal in stabilizing
the crystalline phase and reveal lattice-induced fast crystallization
of the droplet at the initial stage of the coalescence of the nanocrystal
with the droplet. Further sequential observations show the stepped
coalescence and growth mechanism of the nanocrystals at the atomic
scale. These results offer insights into the dynamic process at liquid/solid
interfaces, which may have implications for many functionalities of
materials and their applications
Direct Atomic-Scale Observation of Intermediate Pathways of Melting and Crystallization in Supported Bi Nanoparticles
Uncovering
the evolutional pathways of melting and crystallization
atomically is critical to understanding complex microscopic mechanism
of first-order phase transformation. We conduct in situ atomic-scale
observations of melting and crystallization in supported Bi nanoparticles
under heating and cooling within an aberration-corrected TEM. We provide
direct evidence of the multiple intermediate state events in melting
and crystallization. The melting of the supported nanocrystal involves
the formation and migration of domain boundaries and dislocations
due to the atomic rearrangement under heating, which occurs through
a size-dependent multiple intermediate state. A critical size, which
is key to inducing the transition pathway in melting from two to four
barriers, is identified for the nanocrystal. In contrast, crystallization
of a Bi droplet involves three stages. These findings demonstrate
that the phase transformations cannot be viewed as a simple single
barrier-crossing event but as a complex multiple intermediate state
phenomenon, highlighting the importance of nonlocal behaviors
Estimated continuous annual BCSM rates and hazard ratio of BCSM in certain subpopulations.
<p>(A) Patients were age<40 with ER negative and node positive diseases. (B) Patients were age≥60 with ER positive and node negative diseases.</p
Estimated continuous annual BCSM rates and hazard ratio of BCSM.
<p>A, B & C show estimated continuous annual BCSM rates. The solid line represents patients in cohort 1; the dashed line represents patients in cohort 2.D, E & F show differences of BCSM between patients in the two cohorts. Patients in C1 as reference, the absolute number of decreased BCSM rate (C2 minus C1).G, H & I show hazard ratio of BCSM (Cohort 1 versus cohort 2). Light grey shadows represent 95% CI of survival. HRs with 95% CIs were estimated from the flexible parametric survival models. Curves cut off at 0.5 yrs from diagnosis because of sparse data. Total population: A, D & G; ER negative: B, E & H; ER positive: C, F & I. Notes: Rates were reported per 1000 persons per year; y-axis scales were different in different analyses.</p
Annual BCSM rates and hazard ratio of BCSM in the total population and different subgroups.
<p>Annual BCSM rates and hazard ratio of BCSM in the total population and different subgroups.</p
Real-Time Dynamical Observation of Lattice Induced Nucleation and Growth in Interfacial Solid–Solid Phase Transitions
Uncovering
dynamical processes of lattice induced epitaxial growth
of nanocrystal on the support is critical to understanding crystallization,
solid-phase epitaxial growth, Oswald ripening process, and advanced
nanofabrication, all of which are linked to different important applications
in the materials field. Here, we conduct direct <i>in situ</i> atomic-scale dynamical observation of segregated Bi layers on SrBi<sub>2</sub>Ta<sub>2</sub>O<sub>9</sub> support under low dose electron
irradiation to explore the nucleation and growth from an initial disordered
solid state to a stable faceted crystal by using aberration-corrected
transmission electron microscopy. We provide, for the first time,
atomic-scale insights into the initial prenucleation stage of lattice
induced interfacial nucleation, size-dependent crystalline fluctuation,
and stepped-growth stage of the formed nanocrystal on the oxide support
at the atomic scale. We identify a critical diameter in forming a
stable faceted configuration and find interestingly that the stable
nanocrystal presents a size-dependent coalescence mechanism. These
results offer an atomic-scale view into the dynamic process at solid/solid
interfaces, which has implications for thin film growth and advanced
nanofabrication
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