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Error: #f88
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body {font-size:.75em; font-family:arial,helvetica; margin:0; padding:0;}

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h3 {font-size:1.1em;}
h4 {font-size:1em;}
h5 {font-size:.9em;}

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dt {font-weight:bold;}

ol {list-style-type:decimal;}
ol ol {list-style-type:lower-alpha;}
ol ol ol {list-style-type:lower-roman;}
ol ol ol ol {list-style-type:decimal;}
ol ol ol ol ol {list-style-type:lower-alpha;}
ol ol ol ol ol ol {list-style-type:lower-roman;}
ol ol ol ol ol ol ol {list-style-type:decimal;}

.txtOptionInput {width:11em;}

#contentWrapper .chkOptionInput {border:0;}

.externalLink {text-decoration:underline;}

.indent {margin-left:3em;}
.outdent {margin-left:3em; text-indent:-3em;}
code.escaped {white-space:nowrap;}

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.tiddlyLinkNonExisting {font-style:italic;}

/* the 'a' is required for IE, otherwise it renders the whole tiddler in bold */
a.tiddlyLinkNonExisting.shadow {font-weight:bold;}

#mainMenu .tiddlyLinkExisting,
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#sidebarTabs .tiddlyLinkExisting {font-weight:bold; font-style:normal;}

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.header a:hover {background:transparent;}
.headerShadow {position:relative; padding:4.5em 0 1em 1em; left:-1px; top:-1px;}
.headerForeground {position:absolute; padding:4.5em 0 1em 1em; left:0px; top:0px;}

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.siteSubtitle {font-size:1.2em;}

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.messageToolbar {display:block; text-align:right; padding:0.2em;}
#messageArea a {text-decoration:underline;}

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.tabContents {padding:0.5em;}
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.tagClear {clear:both;}

.footer {font-size:.9em;}
.footer li {display:inline;}

.annotation {padding:0.5em; margin:0.5em;}

* html .viewer pre {width:99%; padding:0 0 1em 0;}
.viewer {line-height:1.4em; padding-top:0.5em;}
.viewer .button {margin:0 0.25em; padding:0 0.25em;}
.viewer blockquote {line-height:1.5em; padding-left:0.8em;margin-left:2.5em;}
.viewer ul, .viewer ol {margin-left:0.5em; padding-left:1.5em;}

.viewer table, table.twtable {border-collapse:collapse; margin:0.8em 1.0em;}
.viewer th, .viewer td, .viewer tr,.viewer caption,.twtable th, .twtable td, .twtable tr,.twtable caption {padding:3px;}
table.listView {font-size:0.85em; margin:0.8em 1.0em;}
table.listView th, table.listView td, table.listView tr {padding:0px 3px 0px 3px;}

.viewer pre {padding:0.5em; margin-left:0.5em; font-size:1.2em; line-height:1.4em; overflow:auto;}
.viewer code {font-size:1.2em; line-height:1.4em;}

.editor {font-size:1.1em;}
.editor input, .editor textarea {display:block; width:100%; font:inherit;}
.editorFooter {padding:0.25em 0; font-size:.9em;}
.editorFooter .button {padding-top:0px; padding-bottom:0px;}

.fieldsetFix {border:0; padding:0; margin:1px 0px;}

.sparkline {line-height:1em;}
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.zoomer {font-size:1.1em; position:absolute; overflow:hidden;}
.zoomer div {padding:1em;}

* html #backstage {width:99%;}
* html #backstageArea {width:99%;}
#backstageArea {display:none; position:relative; overflow: hidden; z-index:150; padding:0.3em 0.5em;}
#backstageToolbar {position:relative;}
#backstageArea a {font-weight:bold; margin-left:0.5em; padding:0.3em 0.5em;}
#backstageButton {display:none; position:absolute; z-index:175; top:0; right:0;}
#backstageButton a {padding:0.1em 0.4em; margin:0.1em;}
#backstage {position:relative; width:100%; z-index:50;}
#backstagePanel {display:none; z-index:100; position:absolute; width:90%; margin-left:3em; padding:1em;}
.backstagePanelFooter {padding-top:0.2em; float:right;}
.backstagePanelFooter a {padding:0.2em 0.4em;}
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/*}}}*/
/***
StyleSheet for use when a translation requires any css style changes.
This StyleSheet can be used directly by languages such as Chinese, Japanese and Korean which need larger font sizes.
***/
/*{{{*/
body {font-size:0.8em;}
#sidebarOptions {font-size:1.05em;}
#sidebarOptions a {font-style:normal;}
#sidebarOptions .sliderPanel {font-size:0.95em;}
.subtitle {font-size:0.8em;}
.viewer table.listView {font-size:0.95em;}
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/*{{{*/
@media print {
#mainMenu, #sidebar, #messageArea, .toolbar, #backstageButton, #backstageArea {display: none !important;}
#displayArea {margin: 1em 1em 0em;}
noscript {display:none;} /* Fixes a feature in Firefox 1.5.0.2 where print preview displays the noscript content */
}
/*}}}*/
<!--{{{-->
<div class='header' macro='gradient vert [[ColorPalette::PrimaryLight]] [[ColorPalette::PrimaryMid]]'>
<div class='headerShadow'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>&nbsp;
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
<div class='headerForeground'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>&nbsp;
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
</div>
<div id='mainMenu' refresh='content' tiddler='MainMenu'></div>
<div id='sidebar'>
<div id='sidebarOptions' refresh='content' tiddler='SideBarOptions'></div>
<div id='sidebarTabs' refresh='content' force='true' tiddler='SideBarTabs'></div>
</div>
<div id='displayArea'>
<div id='messageArea'></div>
<div id='tiddlerDisplay'></div>
</div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
<div class='tagging' macro='tagging'></div>
<div class='tagged' macro='tags'></div>
<div class='viewer' macro='view text wikified'></div>
<div class='tagClear'></div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::EditToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='editor' macro='edit title'></div>
<div macro='annotations'></div>
<div class='editor' macro='edit text'></div>
<div class='editor' macro='edit tags'></div><div class='editorFooter'><span macro='message views.editor.tagPrompt'></span><span macro='tagChooser excludeLists'></span></div>
<!--}}}-->
To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers:
* [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* [[MainMenu]]: The menu (usually on the left)
* [[DefaultTiddlers]]: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>
These [[InterfaceOptions]] for customising [[TiddlyWiki]] are saved in your browser

Your username for signing your edits. Write it as a [[WikiWord]] (eg [[JoeBloggs]])

<<option txtUserName>>
<<option chkSaveBackups>> [[SaveBackups]]
<<option chkAutoSave>> [[AutoSave]]
<<option chkRegExpSearch>> [[RegExpSearch]]
<<option chkCaseSensitiveSearch>> [[CaseSensitiveSearch]]
<<option chkAnimate>> [[EnableAnimations]]

----
Also see [[AdvancedOptions]]
<<importTiddlers>>
[[Research Topics]]
[[Members of the Group]]
[[Recent Publications]]
[[Theoretical Chemistry at UCI]]
[[Research Topics]]
[[Members of the Group]]
[[Recent Publications]]
[[Theoretical Chemistry at UCI]]
!!!Professor
[[Ioan Andricioaei|http://www.chem.uci.edu/people/ioan-andricioaei]]

!!!Postdocs:
Jason Deckman

!!!Graduate Students:
Gavin Bascom
Emel Ficici
Gianmarc Johns
Ahmet Mentes
Nick Preketes (joint with Professor Shaul Mukamel)
Mahua Roy
Maryna Taranova

!!!Undergraduate Assistants:
Open positions

D. Jeong and I. Andricioaei, “Reconstructing equilibrium entropy and enthalpy profiles from non-equilibrium pulling,” J. Chem. Phys. 138, 114110 (2013) [[link|http://dx.doi.org/10.1063/1.4795236]] 

A. D. Hirsh, M. Taranova, T. A. Lionberger, T. D. Lillian, I. Andricioaei* and N. Perkins*, “Structural Ensemble and Dynamics of Toroidal-like DNA Shapes in Bacteriophage Phi29 Exit Cavity,” Biophys. J. 104, 2058-2067 (2013) [[link|http://dx.doi.org/10.1016/j.bpj.2013.03.032]]

Loïc Salmon, Gavin Bascom, Ioan Andricioaei, and Hashim M. ~Al-Hashimi, "A General Method for Constructing ~Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed," J. Am. Chem. Soc. 135, 5457-5466 (2013) [[link|http://dx.doi.org/10.1021/ja400920w]]

A. T. Frank and S. Horowitz and I. Andricioaei* and H.M. ~Al-Hashimi*, “Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics,” J. Phys. Chem. B, 117, 2045-2052 (2013). [[link|http://dx.doi.org/10.1021/jp310863c]]

M. Mills, B. Orr, M.M. Banaszak Holl and I. Andricioaei, “Attractive hydration forces in ~DNA-dendrimer Interactions at the nanometer scale,” J. Phys. Chem. B, 117, 973-981 (2013). [[link|http://dx.doi.org/10.1021/jp309616t]] 
 
E. N. Nikolova, G. Bascom, I. Andricioaei and H. M. ~Al-Hashimi, “Probing sequence-specific DNA flexibility in A-tracts and pyrimidine-purine steps by NMR 13C relaxation and MD simulations,” Biochemistry 51, 8654 (2012) [[link|http://pubs.acs.org/doi/abs/10.1021/bi3009517]]. 
 
P. P. Jose and I. Andricioaei, Similarities between protein folding and granular jamming, Nature Communications 3, 1161 (2012) [[link|http://www.nature.com/ncomms/journal/v3/n10/full/ncomms2177.html]]. 
 
N. K. Preketes, J. D. Biggs, H. Ren, I. Andricioaei and S. Mukamel, Simulations of two-dimensional infrared and stimulated resonance Raman spectra of photoactive yellow protein, Chemical Physics, (2012) [[link|http://dx.doi.org/10.1016/j.chemphys.2012.09.002]].
 
A. Boughton, K. Nguyen, I. Andricioaei* and Z. Chen*, Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies, Langmuir 27, 14343-14351 (2011) [[link|http://pubs.acs.org/doi/abs/10.1021/la203192c]]. 
 
T. D. Lillian, M. Taranova, J. Wereszczynski, I. Andricioaei*, and N. C. Perkins*. “A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB,” Biophys. J., 100, 2016–2023 (2011) [[link|http://www.cell.com/biophysj/retrieve/pii/S0006349511003122]]. 

A.C. Stelzer, A.T. Frank, J.D. Kratz, M.D. Swanson, M.J. ~Gonzalez-Hernandez, J. Lee, I. Andricioaei, D.M. Markovitz and H.M. ~Al-Hashimi, "Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble," Nature Chem. Biol. 7, 553–559 (2011)  [[link|http://www.nature.com/nchembio/journal/v7/n8/full/nchembio.596.html]].

E. Nikolova, E. Kim, A. Wise, P. O’Brien, I. Andricioaei and H.M. ~Al-Hashimi, "Transient Hoogsteen Base-pairs in Canonical Duplex DNA," Nature 470, 498–502 (2011) [[link|http://www.nature.com/nature/journal/v470/n7335/full/nature09775.html]].

A.T. Frank, I. Andricioaei, "A Comparative Study on the Ability of Two Implicit Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles," J. Membrane Biol. 239, 57-62 (2011) [[pdf|reprints/FrankA11.pdf]].

A.P. Boughton, I. Andricioaei and Z. Chen, "Surface Orientation of Magainin 2: Molecular Dynamics Simulation and Sum Frequency Generation Vibrational Spectroscopic Studies," Langmuir, 26, 16031-16036 (2010) [[pdf|reprints/BoughtonAC10.pdf]].

J. Wereszczynski and I. Andricioaei, "Free Energy Calculations Reveal ~Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition," Biophys. J. 99, 869–878 (2010) [[pdf|reprints/WereszczynskiA10-BiophysJ.pdf]].

J. Wereszczynski and I. Andricioaei, "Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic ~Acid-Based Nanothermometers," J. Phys. Chem. B 114, 2076-2082 (2010) [[pdf|reprints/WereszczynskiA10.pdf]].

M. Mills, B. Orr, M.M. Banaszak Holl and I. Andricioaei, "Microscopic Basis for the Mesoscopic Extensibility of ~Dendrimer-Compacted DNA," Biophys. J. 98, 834-842 (2010) [[pdf|reprints/MillsOBA10.pdf]].

C. Musselman, Q. Zhang, H.M. ~Al-Hashimi and I. Andricioaei, “Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA,” J. Phys. Chem. B 114, 929-939 (2010) [[pdf|reprints/MusselmanZAA10.pdf]].

A.C. Stelzer, A.T. Frank, M. Bailor, H.M. ~Al-Hashimi and I. Andricioaei,  “Constructing ~Atomic-Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR ~RDCs,” Methods 49, 167-173 (2009).

A.T. Frank, A.C. Stelzer, H.M. ~Al-Hashimi and I. Andricioaei, “Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR ~RDCs: New insights into RNA dynamics and adaptive ligand recognition,” Nucleic Acids Res. 37, 3670-3679 (2009) [[pdf|reprints/FrankSAA09.pdf]].

J. Nummela and I. Andricioaei, “Energy landscape for DNA rotation and sliding through a phage portal,” Biophys.J. (Letter) 96, ~L29-L31 (2009) [[pdf|reprints/NummelaA09.pdf]].

M. Mills and I. Andricioaei, “An experimentally guided umbrella sampling protocol for biomolecules,” J. Chem. Phys. 129,114101 (2008) [[pdf|reprints/MillsA08.pdf]].

E. Dethoff, A. Hansen, C. Musselman, E. Watt, I. Andricioaei, and H.M. ~Al-Hashimi, “Characterizing Complex Dynamics in the TAR Apical Loop and Motional Correlations with the Bulge by NMR, MD and Mutagenesis,” Biophys. J. 95, 3906-3915 (2008).

C.V. Kelly, P. R. Leroueil, E.K. Nett, J. M. Wereszczynski, J.R. Baker, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers I: Free Energy and Conformation of Binding," J. Phys. Chem. B 112, 9337-9345 (2008) [[pdf|reprints/KellyLNWBOHA08.pdf]].

C.V. Kelly, P. R. Leroueil, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers II: Effects of Bilayer Phase and Dendrimer Termination," J. Phys. Chem. B 112, 9346-9353 (2008) [[pdf|reprints/KellyLOHA08.pdf]].

J. Nummela, F. Yassin and I. Andricioaei, “Entropy-energy decomposition from nonequilibrium work trajectories,” J. Chem. Phys. 128, 024104 (2008) [[pdf|reprints/NummelaYA08.pdf]].

J. ~MacFadyen, J. Wereszczynski and I. Andricioaei, “Directionally negative friction: A method for enhanced sampling of rare events,” J. Chem. Phys. 128, 114112 (2008) [[pdf|reprints/MacFadyenWA08.pdf]].

J. Nummela and I. Andricioaei, “Exact low-force kinetics from high-force single-molecule unfolding events,” Biophys. J. 93, 3373-3381 (2007) [[pdf|reprints/NummelaA07.pdf]].

C. Musselman, H.M. ~Al-Hashimi and I. Andricioaei, “iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a   dynamical hinge," Biophys. J. 93, 411-422 (2007) [[pdf|reprints/MusselmanAA07.pdf]].

D.M. Jordan, M. Mills, I. Andricioaei, K. Palmo and E.R.P. Zuiderweg, “Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations: Effects of dynamic local distortions on 13C carbonyl NMR relaxation,” Chem. Phys. Chem. 8, 1375-1385 (2007).

I. Andricioaei, “Specialized methods for improving ergodic sampling using molecular dynamics and Monte Carlo simulations” in Free Energy Calculations: Theory and Applications in Chemistry and Biology, pp. 277-322, eds. A. Pohorille and C. Chipot, Springer Series in Chemical Physics, (2007).

J. Wereszczynski and I. Andricioaei, “On structural transitions, thermodynamic equilibrium and the phase diagram of DNA and RNA duplexes under external tension and torque," Proc. Natl. Acad. Sci. U.S.A. 103, 16200-16205 (2006) [[pdf|reprints/WereszczynskiA06.pdf]].

C. Musselman, S. Pitt, K. Gulati, L. Foster, I. Andricioaei and H. ~Al-Hashimi, “Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings” J. Biomol. NMR, 36, 235-249 (2006).

P. Tian and I. Andricioaei, “Size, motion and function of the ~SecY translocon revealed by molecular dynamics simulations with virtual probes,” Biophys. J., 90, 2718-2730 (2006) [[pdf|reprints/TianA06.pdf]].

C. Xing and I. Andricioaei, “On the calculation of time-correlation functions by potential scaling,” J. Chem. Phys. 124, 034110 (2006) [[pdf|reprints/XingA06.pdf]].

G. Luo, I. Andricioaei, X.S. Xie and M. Karplus, "Distance disorder in proteins is caused by trapping,” (Letter) J. Phys. Chem. B 110, 9363-9367 (2006) [[pdf|reprints/LuoAXK06.pdf]].

J. ~MacFadyen and I. Andricioaei, “A ~Skewed-Momenta method to efficiently generate conformational-transition trajectories,” J. Chem. Phys. 123, 074107 (2005) [[pdf|reprints/MacFadyenA05.pdf]].

L. Sari and I. Andricioaei, “Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative DNA supercoil relaxation” Nucleic Acids Research 33, 6621-6634 (2005) [[pdf|reprints/SariA05.pdf]].

P. Tian and I. Andricioaei, “Repetitive pulling catalyzes co-translocational unfolding of barnase during import through a mitochondrial pore,” J. Mol. Biol. 350, 1017-1034 (2005) [[pdf|reprints/TianA05.pdf]].

M. Jin, I. Andricioaei, T.A. Springer, “Conversion between three conformational states of integrin I domains with a C-terminal pull spring studied with molecular dynamics,” Structure 12, 2137-2147 (2004).

We are a research group interested in theoretical chemistry and computational molecular biophysics affiliated with the [[Department of Chemistry|http://www.chem.uci.edu]] in the School of [[Physical Sciences|http://ps.uci.edu]] of the University of California, Irvine.

Our research explores theoretical topics at the interface between molecular biophysics and physical chemistry. It hinges on a two-fold central theme: (1) developing novel theoretical techniques and (2) applying computer and modeling methods to describe, in terms of dynamics and thermodynamics, biologically important molecular processes, with the aim to explain or predict experimental findings. Research directions include:

!!!Enhanced Sampling in Trajectory Space. 
Many important equilibrium and kinetic properties of chemical systems (including proteins and nucleic acids) can be cast in terms of paths in multi-dimensional spaces. Sampling and optimization algorithms we have developed for the conformational space can be generalized and adapted to the space of paths. We see fertile ground for theoretical and computational work on several categories of paths, from chemical-reaction paths to paths in the sequence space of evolving proteins. We have developed a set of trajectory reweighting techniques based on a stochastic path integral formalism that is particularly useful to treat both computer simulations and single-molecule experimental traces.

!!!Computer Simulations of ~DNA-Binding Machines. 
~Protein-DNA interactions are essential in such crucial cellular functions as replication, repair, transcription or recombination. Many enzymes at and ahead of the replication fork affect large DNA fragments. For instance, topoisomerases undo DNA knotting. Others, like helicases and polymerases, are biomolecular motors: they use the energy of binding and/or hydrolysis of nucleotides to do mechanical work on the DNA fragments to which they bind. Another example is the machinery that compacts DNA inside the capsid of viruses. We have an avid interest in the theoretical description of these fundamental genetic processes through massively parallel computer simulations; here are a few highlights of our work from supercomputing agencies [[TeraGrid|http://www.tacc.utexas.edu/feature_stories/2008/recipes_for_replication.php]], [[NERSC|http://www.nersc.gov/news/nerscnews/NERSCNews_2008_03.pdf]], [[Cray|http://www.cray.com/Assets/PDF/successstories/DNA_nanoparticles.pdf]].

!!!~Dynamics-Function Relationships. Connections to NMR Relaxation. 
An accurate measure of free energy, important for protein or RNA stability and function, or for ligand binding, has to include the entropy manifested in molecular flexibility. On the experimental side, this dynamic aspect is brought in by developments in solution NMR spectroscopy, which measures motion by relaxation experiments. Molecular dynamics simulation is an important tool to complement these measurements and to connect dynamics to entropy.


The Andricioaei Group at UCI
Keeping in line with the prominent status of its other highly-ranked programs, the Department of Chemistry at UCI has identified Theoretical Chemistry as a focus of growth and has established a center of excellence for [[Theoretical Chemistry|http://www.chem.uci.edu/research/areas/theoretical-and-computational]]. Research topics in the theory groups are covering all major sub-fields of modern chemical theory. Current theoretical and computational research at UCI includes methodology for quantum dynamics simulation, theoretical spectroscopy, femtochemistry, electronic structure, statistical mechanics, biomolecular structure and dynamics, atmospheric chemistry, nanotechnology, foundations of quantum mechanics and quantum information theory, and signal processing. 

[[UCI|http://www.uci.edu]] combines the strengths of a top-tier research university with the bounty of an incomparable Southern California [[location|http://en.wikipedia.org/wiki/Orange_County,_California]]; students interested in our newly established Theoretical Chemistry Ph.D. track should contact the program faculty directly. 

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