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Quantum and Classical Molecular Dynamics

PGR-P-109

Key facts

Type of research degree
PhD
Application deadline
Ongoing deadline
Country eligibility
International (open to all nationalities, including the UK)
Funding
Competition funded
Supervisors
Professor Dmitry Shalashilin
Schools
School of Chemistry
<h2 class="heading hide-accessible">Summary</h2>

There are two main research projects available. First project is focused on quantum dynamics in chemistry and physics. Second project is focused on classical Molecular Dynamics (MD) of biological molecules such as proteins and peptides 1 Chemistry is about rearranging nuclei whose motion is often quantum. Understanding tunnelling, zero point energy, quantization of vibrational and rotational motions and transitions between electronic states is crucial for chemical dynamics. We develop new techniques which speed up quantum simulations and allow to treat larger molecular systems 1-3. The main idea is to use classical mechanics to guide quantum basis, which is illustrated on the figure below showing a trajectory guided grid following the wave function 2 Classical MD disregards quantum effects but can treat realistic molecular systems comprised of thousands of atoms. The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude has to be bridged. We developed efficient methods which allow to solve this problem by recovering long time dynamics from a set of short time simulations.

<h2 class="heading hide-accessible">Full description</h2>

<p>In 1929 Dirac stated that: &ldquo;<a href="http://www.brainyquote.com/quotes/quotes/p/pauldirac279318.html" title="view quote">The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved.</a>&rdquo; Only recently however, many years later, have atomistic simulation methods started to emerge that allow the treatment of quantum systems with many degrees of freedom, overcoming the difficulty noted by Dirac. Leeds Quantum and Classical Molecular Dynamics group develops new computational methods for atomistic simulations in chemistry and physics.&nbsp; These methods can treat bigger molecular systems faster and more accurately. &nbsp;They can visualise what happens at in atomic and molecular level. &nbsp;</p> <p>There are two main research projects available. First project is focused on&nbsp;<strong><em>quantum dynamics</em></strong>&nbsp;in chemistry and physics. Chemistry is about rearranging nuclei whose motion is often quantum.&nbsp; Understanding tunnelling, zero point energy, quantization of vibrational and rotational motions and transitions between electronic states is crucial for chemical dynamics.&nbsp; We develop new techniques which speed up quantum simulations and allow to treat larger molecular systems1-3.&nbsp; The main idea is to use classical mechanics to guide quantum basis, which is illustrated on the figure below showing a trajectory guided grid following the wave function</p> <p>We developed several methods, which exploit this very simple idea, and applied them to many interesting problems in chemistry and physics which range from chemical dynamics on ultrafast femtosecond time scale&nbsp;to dynamics of electrons in laser field&nbsp;and even quantum computers.</p> <p>Second project is focused on&nbsp;<strong><em>classical Molecular Dynamics (MD) of biological molecules</em></strong>&nbsp;such as proteins and peptides.&nbsp; Classical MD disregards quantum effects but can treat realistic molecular systems comprised of thousands of atoms. &nbsp;The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude has to be bridged.&nbsp; We developed efficient methods which allow to solve this problem by recovering long time dynamics from &nbsp;a set of short time simulations.&nbsp;</p> <p>&nbsp; We apply our methods of accelerated classical MD to the investigation of protein unfolding, and peptide cyclization. &nbsp;For example with the help of our new methods we work on computational design of cyclic peptides, which currently are considered as prospective new antibiotics and anticancer drugs.</p> <p>Our research is very mathematical and involves the use of powerful computers.&nbsp; Both projects are suited not only for chemists but also for physics and mathematics graduates.&nbsp;</p> <p>Further information about our&nbsp;<a href="Quantum and Classical Molecular Dynamics Project">Quantum and Classical Molecular Dynamics Project</a>&nbsp;(PDF)</p> <p>The earliest start date for this project will be 1 October 2020.&nbsp;</p> <p>&nbsp;</p>

<h2 class="heading">How to apply</h2>

<p>Formal applications for research degree study should be made online through the&nbsp;<a href="https://www.leeds.ac.uk/info/130206/applying/91/applying_for_research_degrees">University&#39;s website</a>. Please state clearly in the research information section&nbsp;that the research degree you wish to be considered for is &lsquo;Quantum and Classical Molecular Dynamics&rsquo; as well as&nbsp;<a href="https://physicalsciences.leeds.ac.uk/staff/197/professor-dmitry-shalashilin">Professor Dmitry Shalashilin</a>&nbsp;as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p> <p><em>We welcome applications from all suitably-qualified candidates, but UK black and minority ethnic (BME) researchers are currently under-represented in our Postgraduate Research community, and we would therefore particularly encourage applications from UK BME candidates. All scholarships will be awarded on the basis of merit.</em></p>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

<p><strong>Self-Funding Students</strong></p> <p><strong>Funding Eligibility</strong></p> <p><strong>UK/EU</strong> &ndash;&nbsp;Leeds Doctoral Scholarship Award paying Academic Fees and Maintenance matching EPSRC rate of &pound;15,009 per year for 3 years, Lowson Research Scholarship&nbsp;paying Academic Fees and Maintenance at a fixed rate of &pound;14,000 per year for 3 years.&nbsp; Alumni Bursary is available for previous graduates from the University of Leeds offering 10% discount on Academic Fees only.</p> <p><strong>International Students</strong> &ndash;&nbsp;China Scholarship Council-University of Leeds Scholarship Award paying Academic Fees for 3 years, Commonweath PhD and Commonwealth Split-Site Scholarships for Low and Middle Income countries.&nbsp; Alumni Bursary is available for previous graduates from the University of Leeds offering 10% discount on Academic Fees only.</p>

<h2 class="heading">Contact details</h2>

<p>For further information regarding your application, please contact Doctoral College Admissions by&nbsp;email: <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions</a><a href="mailto:EMAIL@leeds.ac.uk">@leeds.ac.uk</a>, or by telephone: +44 (0)113 343 5057.</p> <p>For further information regarding the project, please contact Professor Dmitry Shalashilin by email:&nbsp;&nbsp;<a href="mailto:D.Shalashilin@leeds.ac.uk">D.Shalashilin@leeds.ac.uk</a></p>


<h3 class="heading heading--sm">Linked funding opportunities</h3>